=>> Building biology/seqan-apps build started at Sat Dec 6 02:52:59 EST 2025 port directory: /usr/ports/biology/seqan-apps package name: seqan-apps-2.4.0_11 building for: FreeBSD pkg.DaveG.ca 15.0-RC3 FreeBSD 15.0-RC3 amd64 maintained by: h2+fbsdports@fsfe.org Makefile datestamp: -rw-r--r-- 1 root wheel 1045 Aug 27 2024 /usr/ports/biology/seqan-apps/Makefile Ports top last git commit: 62d8b1999233 Ports top unclean checkout: no Port dir last git commit: 6d558714dfde Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RC3 UNAME_r=15.0-RC3 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for seqan-apps-2.4.0_11: ====> Options available for the radio ARCH: you can only select none or one of them SSE4=off: Use SSE4 and POPCNT instructions AVX2=off: Use SSE4, AVX2 and POPCNT instructions NATIVE=off: Use all available instruction sets (-march=native) ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- h2+fbsdports@fsfe.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work/.cache HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work/.cache HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 " CXXSTD=c++14 BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" RM_I386="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/seqan-apps" EXAMPLESDIR="share/examples/seqan-apps" DATADIR="share/seqan-apps" WWWDIR="www/seqan-apps" ETCDIR="etc/seqan-apps" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqan-apps DOCSDIR=/usr/local/share/doc/seqan-apps EXAMPLESDIR=/usr/local/share/examples/seqan-apps WWWDIR=/usr/local/www/seqan-apps ETCDIR=/usr/local/etc/seqan-apps --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> seqan-apps-2.4.0_11 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> seqan-apps-2.4.0_11 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-apps-2.4.0_11 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building => SHA256 Checksum OK for seqan-seqan-seqan-v2.4.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building ===> Extracting for seqan-apps-2.4.0_11 => SHA256 Checksum OK for seqan-seqan-seqan-v2.4.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for seqan-apps-2.4.0_11 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> seqan-apps-2.4.0_11 depends on package: boost-libs>0 - not found ===> Installing existing package /packages/All/boost-libs-1.89.0_1.pkg [pkg.DaveG.ca] Installing boost-libs-1.89.0_1... [pkg.DaveG.ca] `-- Installing icu-76.1,1... [pkg.DaveG.ca] `-- Extracting icu-76.1,1: .......... done [pkg.DaveG.ca] `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] Extracting boost-libs-1.89.0_1: .......... done ===== Message from boost-libs-1.89.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> seqan-apps-2.4.0_11 depends on package: boost-libs>0 - found ===> Returning to build of seqan-apps-2.4.0_11 ===> seqan-apps-2.4.0_11 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.9.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.9... [pkg.DaveG.ca] `-- Installing expat-2.7.3... [pkg.DaveG.ca] `-- Extracting expat-2.7.3: .......... done [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Installing libunistring-1.4.1... [pkg.DaveG.ca] | `-- Extracting libunistring-1.4.1: .......... done [pkg.DaveG.ca] `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] `-- Installing libuv-1.51.0... [pkg.DaveG.ca] `-- Extracting libuv-1.51.0: .......... done [pkg.DaveG.ca] `-- Installing rhash-1.4.4_2... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] `-- Extracting rhash-1.4.4_2: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.9: .......... done ===> seqan-apps-2.4.0_11 depends on file: /usr/local/bin/cmake - found ===> Returning to build of seqan-apps-2.4.0_11 ===> seqan-apps-2.4.0_11 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.13.1,4.pkg [pkg.DaveG.ca] Installing ninja-1.13.1,4... [pkg.DaveG.ca] `-- Installing python311-3.11.14... [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.1... [pkg.DaveG.ca] | `-- Extracting readline-8.3.1: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] Extracting ninja-1.13.1,4: ..... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> seqan-apps-2.4.0_11 depends on executable: ninja - found ===> Returning to build of seqan-apps-2.4.0_11 ===> seqan-apps-2.4.0_11 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> seqan-apps-2.4.0_11 depends on file: /usr/local/bin/ccache - found ===> Returning to build of seqan-apps-2.4.0_11 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for seqan-apps-2.4.0_11 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/seqan-apps/work/.build CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The CXX compiler identification is Clang 19.1.7 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Initializing SeqAn Build System... -- Selected repository dir: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0 -- No revision system found. -- Repository date not determined. -- Repository revision not determined. -- Configuring apps CMake Deprecation Warning at apps/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at apps/alf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/alf -- Performing Test CXX14_BUILTIN -- Performing Test CXX14_BUILTIN - Success CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/alf/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/bs_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/bs_tools -- Found ZLIB: /usr/lib/libz.so (found version "1.3.1") CMake Warning (dev) at apps/bs_tools/CMakeLists.txt:27 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/local/include (found version "1.89.0") CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/bs_tools/CMakeLists.txt:28 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/bs_tools/CMakeLists.txt:123 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/dfi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/dfi CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/dfi/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/dfi/CMakeLists.txt:74 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/fiona/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/fiona -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") -- Found OpenMP: TRUE (found version "5.1") CMake Warning (dev) at apps/fiona/CMakeLists.txt:23 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/fiona/CMakeLists.txt:24 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/fiona/CMakeLists.txt:100 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/fx_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/fx_tools CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/fx_tools/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/gustaf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/gustaf CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/gustaf/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/gustaf/CMakeLists.txt:97 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/insegt/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/insegt CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/insegt/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/insegt/CMakeLists.txt:88 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/mason2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/mason2 CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/mason2/CMakeLists.txt:23 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/mason2/CMakeLists.txt:167 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/micro_razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/micro_razers CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/micro_razers/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/micro_razers/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/ngs_roi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/ngs_roi CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/ngs_roi/CMakeLists.txt:23 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/ngs_roi/CMakeLists.txt:114 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/pair_align/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/pair_align CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/pair_align/CMakeLists.txt:26 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/pair_align/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/param_chooser/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/param_chooser CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/param_chooser/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/rabema/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/rabema CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/rabema/CMakeLists.txt:22 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/rabema/CMakeLists.txt:110 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/razers CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/razers/CMakeLists.txt:26 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers/CMakeLists.txt:90 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/razers3/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/razers3 -- Found BZip2: /usr/lib/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/razers3/CMakeLists.txt:30 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers3/CMakeLists.txt:112 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers3/CMakeLists.txt:113 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/rep_sep/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/rep_sep CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/rep_sep/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/sak/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/sak CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/sak/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sak/CMakeLists.txt:86 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/sam2matrix/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/sam2matrix CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/sam2matrix/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sam2matrix/CMakeLists.txt:74 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/samcat/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/samcat CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/samcat/CMakeLists.txt:23 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/samcat/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/searchjoin/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/searchjoin CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/searchjoin/CMakeLists.txt:27 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/searchjoin/CMakeLists.txt:79 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/seqan_tcoffee/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/seqan_tcoffee CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/seqan_tcoffee/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/seqan_tcoffee/CMakeLists.txt:73 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/seqcons2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/seqcons2 CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/seqcons2/CMakeLists.txt:22 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/seqcons2/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/sgip/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/sgip CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/sgip/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sgip/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/snp_store/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/snp_store CMake Warning (dev) at apps/snp_store/CMakeLists.txt:22 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/snp_store/CMakeLists.txt:23 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/snp_store/CMakeLists.txt:89 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/splazers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/splazers CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/splazers/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/splazers/CMakeLists.txt:87 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/stellar/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/stellar CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/stellar/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/stellar/CMakeLists.txt:79 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/tree_recon/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/tree_recon CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/tree_recon/CMakeLists.txt:21 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/tree_recon/CMakeLists.txt:73 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") CMake Deprecation Warning at apps/yara/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/yara CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): apps/yara/CMakeLists.txt:27 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/yara/CMakeLists.txt:150 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Unsupported platform FreeBSD, disabling CTD support. -- Configuring done (3.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_C_COMPILER CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/seqan-apps/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for seqan-apps-2.4.0_11 [ 0% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o -MF apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o.d -o apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_tests.cpp FAILED: [code=1] apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o -MF apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o.d -o apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_tests.cpp PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_tests.cpp 1. /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:341:1: current parser token '{' 2. /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:40:1: parsing namespace 'seqan' #0 0x00003fcea2ab60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x00003fcea2ab3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x00003fcea2a643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00003fcea49f22dc (/lib/libthr.so.3+0x1a2dc) #4 0x00003fcea49f18eb (/lib/libthr.so.3+0x198eb) #5 0x00003fce972842d3 ([vdso]+0x2d3) #6 0x00003fce9bec9f48 clang::Parser::ParseClassSpecifier(clang::tok::TokenKind, clang::SourceLocation, clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, bool, clang::Parser::DeclSpecContext, clang::ParsedAttributes&) (/usr/lib/libprivateclang.so.19+0x2cc9f48) #7 0x00003fce9beaa676 clang::Parser::ParseDeclarationSpecifiers(clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, clang::Parser::DeclSpecContext, clang::Parser::LateParsedAttrList*, clang::ImplicitTypenameContext) (/usr/lib/libprivateclang.so.19+0x2caa676) #8 0x00003fce9bf56bab clang::Parser::ParseDeclarationAfterTemplate(clang::DeclaratorContext, clang::Parser::ParsedTemplateInfo&, clang::ParsingDeclRAIIObject&, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d56bab) #9 0x00003fce9bf55c98 clang::Parser::ParseTemplateDeclarationOrSpecialization(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d55c98) #10 0x00003fce9bf555ec clang::Parser::ParseDeclarationStartingWithTemplate(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&) (/usr/lib/libprivateclang.so.19+0x2d555ec) #11 0x00003fce9bea4409 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca4409) #12 0x00003fce9bf66c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #13 0x00003fce9bec2caa clang::Parser::ParseInnerNamespace(llvm::SmallVector const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x2cc2caa) #14 0x00003fce9bec26a1 clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x2cc26a1) #15 0x00003fce9bea4607 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca4607) #16 0x00003fce9bf66c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #17 0x00003fce9bf65368 clang::Parser::ParseTopLevelDecl(clang::OpaquePtr&, clang::Sema::ModuleImportState&) (/usr/lib/libprivateclang.so.19+0x2d65368) #18 0x00003fce9be8fdce clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fdce) #19 0x00003fce9bd21189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #20 0x00003fce9bc9e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #21 0x00003fce9bda779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #22 0x00003fc67597189e (/usr/bin/c+++0xd89e) #23 0x00003fc67597ed53 (/usr/bin/c+++0x1ad53) #24 0x00003fce9b97d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #25 0x00003fcea2a64146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #26 0x00003fce9b97cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #27 0x00003fce9b940af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #28 0x00003fce9b940d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #29 0x00003fce9b95d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #30 0x00003fc67597e4c8 (/usr/bin/c+++0x1a4c8) #31 0x00003fc67597ca92 (/usr/bin/c+++0x18a92) #32 0x00003fcea624e37f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 132 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/mason_tests-be97da.cpp c++: note: diagnostic msg: /tmp/mason_tests-be97da.sh c++: note: diagnostic msg: ******************** [ 1% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp FAILED: [code=1] apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp 1. /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/allocator_multipool.h:72:17: current parser token ';' 2. /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/allocator_multipool.h:42:1: parsing namespace 'seqan' #0 0x000029a956cb60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x000029a956cb3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x000029a956c643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x000029a959cac2dc (/lib/libthr.so.3+0x1a2dc) #4 0x000029a959cab8eb (/lib/libthr.so.3+0x198eb) #5 0x000029a94ca6e2d3 ([vdso]+0x2d3) #6 0x000029a9516c9f48 clang::Parser::ParseClassSpecifier(clang::tok::TokenKind, clang::SourceLocation, clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, bool, clang::Parser::DeclSpecContext, clang::ParsedAttributes&) (/usr/lib/libprivateclang.so.19+0x2cc9f48) #7 0x000029a9516aa676 clang::Parser::ParseDeclarationSpecifiers(clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, clang::Parser::DeclSpecContext, clang::Parser::LateParsedAttrList*, clang::ImplicitTypenameContext) (/usr/lib/libprivateclang.so.19+0x2caa676) #8 0x000029a951756bab clang::Parser::ParseDeclarationAfterTemplate(clang::DeclaratorContext, clang::Parser::ParsedTemplateInfo&, clang::ParsingDeclRAIIObject&, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d56bab) #9 0x000029a951755c98 clang::Parser::ParseTemplateDeclarationOrSpecialization(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d55c98) #10 0x000029a9517555ec clang::Parser::ParseDeclarationStartingWithTemplate(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&) (/usr/lib/libprivateclang.so.19+0x2d555ec) #11 0x000029a9516a4409 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca4409) #12 0x000029a951766c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #13 0x000029a9516c2caa clang::Parser::ParseInnerNamespace(llvm::SmallVector const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x2cc2caa) #14 0x000029a9516c26a1 clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x2cc26a1) #15 0x000029a9516a4607 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca4607) #16 0x000029a951766c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #17 0x000029a951765368 clang::Parser::ParseTopLevelDecl(clang::OpaquePtr&, clang::Sema::ModuleImportState&) (/usr/lib/libprivateclang.so.19+0x2d65368) #18 0x000029a95168fdce clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fdce) #19 0x000029a951521189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #20 0x000029a95149e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #21 0x000029a9515a779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #22 0x000029a12bd2089e (/usr/bin/c+++0xd89e) #23 0x000029a12bd2dd53 (/usr/bin/c+++0x1ad53) #24 0x000029a95117d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #25 0x000029a956c64146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #26 0x000029a95117cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #27 0x000029a951140af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #28 0x000029a951140d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #29 0x000029a95115d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #30 0x000029a12bd2d4c8 (/usr/bin/c+++0x1a4c8) #31 0x000029a12bd2ba92 (/usr/bin/c+++0x18a92) #32 0x000029a95ad1137f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 132 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/pair_align_global-c7eeea.cpp c++: note: diagnostic msg: /tmp/pair_align_global-c7eeea.sh c++: note: diagnostic msg: ******************** [ 2% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o -MF apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o.d -o apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.cpp FAILED: [code=1] apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o -MF apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o.d -o apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.cpp PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.cpp 1. /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_lock.h:61:1: current parser token '{' 2. /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_lock.h:48:1: parsing namespace 'seqan' #0 0x0000217970ab60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x0000217970ab3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x0000217970a643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00002179743562dc (/lib/libthr.so.3+0x1a2dc) #4 0x00002179743558eb (/lib/libthr.so.3+0x198eb) #5 0x000021796779c2d3 ([vdso]+0x2d3) #6 0x000021796bac9f48 clang::Parser::ParseClassSpecifier(clang::tok::TokenKind, clang::SourceLocation, clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, bool, clang::Parser::DeclSpecContext, clang::ParsedAttributes&) (/usr/lib/libprivateclang.so.19+0x2cc9f48) #7 0x000021796baaa676 clang::Parser::ParseDeclarationSpecifiers(clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, clang::Parser::DeclSpecContext, clang::Parser::LateParsedAttrList*, clang::ImplicitTypenameContext) (/usr/lib/libprivateclang.so.19+0x2caa676) #8 0x000021796bb68679 clang::Parser::ParseDeclOrFunctionDefInternal(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d68679) #9 0x000021796bb683a2 clang::Parser::ParseDeclarationOrFunctionDefinition(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d683a2) #10 0x000021796bb673eb clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d673eb) #11 0x000021796bac2caa clang::Parser::ParseInnerNamespace(llvm::SmallVector const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x2cc2caa) #12 0x000021796bac26a1 clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x2cc26a1) #13 0x000021796baa4607 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca4607) #14 0x000021796bb66c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #15 0x000021796bb65368 clang::Parser::ParseTopLevelDecl(clang::OpaquePtr&, clang::Sema::ModuleImportState&) (/usr/lib/libprivateclang.so.19+0x2d65368) #16 0x000021796ba8fdce clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fdce) #17 0x000021796b921189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #18 0x000021796b89e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #19 0x000021796b9a779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #20 0x00002171471af89e (/usr/bin/c+++0xd89e) #21 0x00002171471bcd53 (/usr/bin/c+++0x1ad53) #22 0x000021796b57d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #23 0x0000217970a64146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #24 0x000021796b57cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #25 0x000021796b540af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #26 0x000021796b540d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #27 0x000021796b55d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #28 0x00002171471bc4c8 (/usr/bin/c+++0x1a4c8) #29 0x00002171471baa92 (/usr/bin/c+++0x18a92) #30 0x000021797744437f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 132 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/roi_builder-831219.cpp c++: note: diagnostic msg: /tmp/roi_builder-831219.sh c++: note: diagnostic msg: ******************** [ 2% 64/141] /usr/local/libexec/ccache/c++ -DFIONA_ILLUMINA -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o -MF apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o.d -o apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp FAILED: [code=1] apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o /usr/local/libexec/ccache/c++ -DFIONA_ILLUMINA -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o -MF apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o.d -o apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DFIONA_ILLUMINA -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp 1. /usr/include/c++/v1/string:3462:35: current parser token '{' 2. /usr/include/c++/v1/string:685:1 : parsing namespace 'std' 3. /usr/include/c++/v1/string:685:1 : parsing namespace 'std::__1' #0 0x000037832e0b60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x000037832e0b3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x000037832e0643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x0000378324fc22dc (/lib/libthr.so.3+0x1a2dc) #4 0x0000378324fc18eb (/lib/libthr.so.3+0x198eb) #5 0x00003783248282d3 ([vdso]+0x2d3) #6 0x0000378328cc9f48 clang::Parser::ParseClassSpecifier(clang::tok::TokenKind, clang::SourceLocation, clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, bool, clang::Parser::DeclSpecContext, clang::ParsedAttributes&) (/usr/lib/libprivateclang.so.19+0x2cc9f48) #7 0x0000378328caa676 clang::Parser::ParseDeclarationSpecifiers(clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, clang::Parser::DeclSpecContext, clang::Parser::LateParsedAttrList*, clang::ImplicitTypenameContext) (/usr/lib/libprivateclang.so.19+0x2caa676) #8 0x0000378328d56bab clang::Parser::ParseDeclarationAfterTemplate(clang::DeclaratorContext, clang::Parser::ParsedTemplateInfo&, clang::ParsingDeclRAIIObject&, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d56bab) #9 0x0000378328d55c98 clang::Parser::ParseTemplateDeclarationOrSpecialization(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d55c98) #10 0x0000378328d555ec clang::Parser::ParseDeclarationStartingWithTemplate(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&) (/usr/lib/libprivateclang.so.19+0x2d555ec) #11 0x0000378328ca4409 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca4409) #12 0x0000378328d66c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #13 0x0000378328cc2caa clang::Parser::ParseInnerNamespace(llvm::SmallVector const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x2cc2caa) #14 0x0000378328cc26a1 clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x2cc26a1) #15 0x0000378328ca47cc clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca47cc) #16 0x0000378328d66c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #17 0x0000378328cc2caa clang::Parser::ParseInnerNamespace(llvm::SmallVector const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x2cc2caa) #18 0x0000378328cc26a1 clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x2cc26a1) #19 0x0000378328ca4607 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca4607) #20 0x0000378328d66c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #21 0x0000378328d65368 clang::Parser::ParseTopLevelDecl(clang::OpaquePtr&, clang::Sema::ModuleImportState&) (/usr/lib/libprivateclang.so.19+0x2d65368) #22 0x0000378328c8fdce clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fdce) #23 0x0000378328b21189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #24 0x0000378328a9e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #25 0x0000378328ba779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #26 0x0000377b03e4e89e (/usr/bin/c+++0xd89e) #27 0x0000377b03e5bd53 (/usr/bin/c+++0x1ad53) #28 0x000037832877d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #29 0x000037832e064146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #30 0x000037832877cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #31 0x0000378328740af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #32 0x0000378328740d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #33 0x000037832875d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #34 0x0000377b03e5b4c8 (/usr/bin/c+++0x1a4c8) #35 0x0000377b03e59a92 (/usr/bin/c+++0x18a92) #36 0x00003783352c337f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 132 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/fiona-7e57fb.cpp c++: note: diagnostic msg: /tmp/fiona-7e57fb.sh c++: note: diagnostic msg: ******************** [ 3% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp FAILED: [code=1] apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp 1. /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1707:1: current parser token '{' 2. /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:41:1: parsing namespace 'seqan' #0 0x00001f24458b60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x00001f24458b3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x00001f24458643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00001f244a1e32dc (/lib/libthr.so.3+0x1a2dc) #4 0x00001f244a1e28eb (/lib/libthr.so.3+0x198eb) #5 0x00001f243c4812d3 ([vdso]+0x2d3) #6 0x00001f243fcc9f48 clang::Parser::ParseClassSpecifier(clang::tok::TokenKind, clang::SourceLocation, clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, bool, clang::Parser::DeclSpecContext, clang::ParsedAttributes&) (/usr/lib/libprivateclang.so.19+0x2cc9f48) #7 0x00001f243fcaa676 clang::Parser::ParseDeclarationSpecifiers(clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, clang::Parser::DeclSpecContext, clang::Parser::LateParsedAttrList*, clang::ImplicitTypenameContext) (/usr/lib/libprivateclang.so.19+0x2caa676) #8 0x00001f243fd56bab clang::Parser::ParseDeclarationAfterTemplate(clang::DeclaratorContext, clang::Parser::ParsedTemplateInfo&, clang::ParsingDeclRAIIObject&, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d56bab) #9 0x00001f243fd55c98 clang::Parser::ParseTemplateDeclarationOrSpecialization(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d55c98) #10 0x00001f243fd555ec clang::Parser::ParseDeclarationStartingWithTemplate(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&) (/usr/lib/libprivateclang.so.19+0x2d555ec) #11 0x00001f243fca4409 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca4409) #12 0x00001f243fd66c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #13 0x00001f243fcc2caa clang::Parser::ParseInnerNamespace(llvm::SmallVector const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x2cc2caa) #14 0x00001f243fcc26a1 clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x2cc26a1) #15 0x00001f243fca4607 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca4607) #16 0x00001f243fd66c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #17 0x00001f243fd65368 clang::Parser::ParseTopLevelDecl(clang::OpaquePtr&, clang::Sema::ModuleImportState&) (/usr/lib/libprivateclang.so.19+0x2d65368) #18 0x00001f243fc8fdce clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fdce) #19 0x00001f243fb21189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #20 0x00001f243fa9e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #21 0x00001f243fba779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #22 0x00001f1c1be9789e (/usr/bin/c+++0xd89e) #23 0x00001f1c1bea4d53 (/usr/bin/c+++0x1ad53) #24 0x00001f243f77d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #25 0x00001f2445864146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #26 0x00001f243f77cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #27 0x00001f243f740af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #28 0x00001f243f740d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #29 0x00001f243f75d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #30 0x00001f1c1bea44c8 (/usr/bin/c+++0x1a4c8) #31 0x00001f1c1bea2a92 (/usr/bin/c+++0x18a92) #32 0x00001f244b18537f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 132 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/pair_align_local-092def.cpp c++: note: diagnostic msg: /tmp/pair_align_local-092def.sh c++: note: diagnostic msg: ******************** [ 4% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp FAILED: [code=1] apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp 1. /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/proxy_base.h:68:12: current parser token ';' 2. /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/proxy_base.h:40:1: parsing namespace 'seqan' #0 0x00003a202e0b60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x00003a202e0b3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x00003a202e0643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00003a2031e0d2dc (/lib/libthr.so.3+0x1a2dc) #4 0x00003a2031e0c8eb (/lib/libthr.so.3+0x198eb) #5 0x00003a2023f6e2d3 ([vdso]+0x2d3) #6 0x00003a2027ec9f48 clang::Parser::ParseClassSpecifier(clang::tok::TokenKind, clang::SourceLocation, clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, bool, clang::Parser::DeclSpecContext, clang::ParsedAttributes&) (/usr/lib/libprivateclang.so.19+0x2cc9f48) #7 0x00003a2027eaa676 clang::Parser::ParseDeclarationSpecifiers(clang::DeclSpec&, clang::Parser::ParsedTemplateInfo&, clang::AccessSpecifier, clang::Parser::DeclSpecContext, clang::Parser::LateParsedAttrList*, clang::ImplicitTypenameContext) (/usr/lib/libprivateclang.so.19+0x2caa676) #8 0x00003a2027f56bab clang::Parser::ParseDeclarationAfterTemplate(clang::DeclaratorContext, clang::Parser::ParsedTemplateInfo&, clang::ParsingDeclRAIIObject&, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d56bab) #9 0x00003a2027f55c98 clang::Parser::ParseTemplateDeclarationOrSpecialization(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::AccessSpecifier) (/usr/lib/libprivateclang.so.19+0x2d55c98) #10 0x00003a2027f555ec clang::Parser::ParseDeclarationStartingWithTemplate(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&) (/usr/lib/libprivateclang.so.19+0x2d555ec) #11 0x00003a2027ea4409 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca4409) #12 0x00003a2027f66c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #13 0x00003a2027ec2caa clang::Parser::ParseInnerNamespace(llvm::SmallVector const&, unsigned int, clang::SourceLocation&, clang::ParsedAttributes&, clang::BalancedDelimiterTracker&) (/usr/lib/libprivateclang.so.19+0x2cc2caa) #14 0x00003a2027ec26a1 clang::Parser::ParseNamespace(clang::DeclaratorContext, clang::SourceLocation&, clang::SourceLocation) (/usr/lib/libprivateclang.so.19+0x2cc26a1) #15 0x00003a2027ea4607 clang::Parser::ParseDeclaration(clang::DeclaratorContext, clang::SourceLocation&, clang::ParsedAttributes&, clang::ParsedAttributes&, clang::SourceLocation*) (/usr/lib/libprivateclang.so.19+0x2ca4607) #16 0x00003a2027f66c66 clang::Parser::ParseExternalDeclaration(clang::ParsedAttributes&, clang::ParsedAttributes&, clang::ParsingDeclSpec*) (/usr/lib/libprivateclang.so.19+0x2d66c66) #17 0x00003a2027f65368 clang::Parser::ParseTopLevelDecl(clang::OpaquePtr&, clang::Sema::ModuleImportState&) (/usr/lib/libprivateclang.so.19+0x2d65368) #18 0x00003a2027e8fdce clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fdce) #19 0x00003a2027d21189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #20 0x00003a2027c9e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #21 0x00003a2027da779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #22 0x00003a1802da789e (/usr/bin/c+++0xd89e) #23 0x00003a1802db4d53 (/usr/bin/c+++0x1ad53) #24 0x00003a202797d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #25 0x00003a202e064146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #26 0x00003a202797cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #27 0x00003a2027940af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #28 0x00003a2027940d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #29 0x00003a202795d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #30 0x00003a1802db44c8 (/usr/bin/c+++0x1a4c8) #31 0x00003a1802db2a92 (/usr/bin/c+++0x18a92) #32 0x00003a20343bd37f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 132 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/pair_align_global-dbf874.cpp c++: note: diagnostic msg: /tmp/pair_align_global-dbf874.sh c++: note: diagnostic msg: ******************** [ 4% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.0.11\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/micro_razers/CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -MF apps/micro_razers/CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o.d -o apps/micro_razers/CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/razers/param_tabs.cpp [ 5% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -MF apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o.d -o apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp FAILED: [code=1] apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -MF apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o.d -o apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: In file included from /usr/include/c++/v1/fstream:193: In file included from /usr/include/c++/v1/__locale:24: /usr/include/c++/v1/string:820:42: error: implicit instantiation of undefined template 'std::char_traits' 820 | static_assert(is_same<_CharT, typename traits_type::char_type>::value, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/png_canvas.h:155:38: note: in instantiation of template class 'std::basic_string' requested here 155 | std::basic_string data; | ^ /usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: In file included from /usr/include/c++/v1/fstream:193: In file included from /usr/include/c++/v1/__locale:24: In file included from /usr/include/c++/v1/string:647: /usr/include/c++/v1/string_view:300:42: error: implicit instantiation of undefined template 'std::char_traits' 300 | static_assert(is_same<_CharT, typename traits_type::char_type>::value, | ^ /usr/include/c++/v1/__type_traits/is_convertible.h:30:99: note: in instantiation of template class 'std::basic_string_view' requested here 30 | struct _LIBCPP_TEMPLATE_VIS is_convertible : public integral_constant {}; | ^ /usr/include/c++/v1/string:745:29: note: in instantiation of template class 'std::is_convertible &, std::basic_string_view>' requested here 745 | : public _BoolConstant< is_convertible >::value && | ^ /usr/include/c++/v1/string:1151:27: note: in instantiation of template class 'std::__can_be_converted_to_string_view, std::basic_string>' requested here 1151 | __enable_if_t<__can_be_converted_to_string_view<_CharT, _Traits, _Tp>::value && | ^ /usr/include/c++/v1/string:1154:93: note: while substituting prior template arguments into non-type template parameter [with _Tp = std::basic_string] 1154 | _LIBCPP_METHOD_TEMPLATE_IMPLICIT_INSTANTIATION_VIS _LIBCPP_CONSTEXPR_SINCE_CXX20 explicit basic_string(const _Tp& __t) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1155 | : __r_(__default_init_tag(), __default_init_tag()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1156 | __self_view __sv = __t; | ~~~~~~~~~~~~~~~~~~~~~~~ 1157 | __init(__sv.data(), __sv.size()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1158 | } | ~ /usr/include/c++/v1/string:752:7: note: while substituting deduced template arguments into function template 'basic_string' [with _Tp = std::basic_string, $1 = (no value)] 752 | class basic_string { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/png_canvas.h:153:8: note: while declaring the implicit copy constructor for 'PngIdatChunk' 153 | struct PngIdatChunk | ^ /usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: In file included from /usr/include/c++/v1/fstream:193: In file included from /usr/include/c++/v1/__locale:24: /usr/include/c++/v1/string:2861:5: error: implicit instantiation of undefined template 'std::char_traits' 2861 | traits_type::assign(std::__to_address(__p) + __sz, __n, __c); | ^ /usr/include/c++/v1/string:3302:5: note: in instantiation of member function 'std::basic_string::append' requested here 3302 | append(__n - __sz, __c); | ^ /usr/include/c++/v1/string:1303:84: note: in instantiation of member function 'std::basic_string::resize' requested here 1303 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 void resize(size_type __n) { resize(__n, value_type()); } | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/png_canvas.h:443:24: note: in instantiation of member function 'std::basic_string::resize' requested here 443 | idatChunk.data.resize(height + 4 * canvas.size()); // same as input, should be enough | ^ /usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: In file included from /usr/include/c++/v1/fstream:193: In file included from /usr/include/c++/v1/__locale:24: /usr/include/c++/v1/string:2864:5: error: implicit instantiation of undefined template 'std::char_traits' 2864 | traits_type::assign(__p[__sz], value_type()); | ^ /usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: In file included from /usr/include/c++/v1/fstream:193: In file included from /usr/include/c++/v1/__locale:24: /usr/include/c++/v1/string:2535:5: error: implicit instantiation of undefined template 'std::char_traits' 2535 | traits_type::copy(std::__to_address(__p), std::__to_address(__old_p), __n_copy); | ^ /usr/include/c++/v1/string:2556:3: note: in instantiation of member function 'std::basic_string::__grow_by' requested here 2556 | __grow_by(__old_cap, __delta_cap, __old_sz, __n_copy, __n_del, __n_add); | ^ /usr/include/c++/v1/string:2858:7: note: in instantiation of member function 'std::basic_string::__grow_by_without_replace' requested here 2858 | __grow_by_without_replace(__cap, __sz + __n - __cap, __sz, __sz, 0); | ^ /usr/include/c++/v1/string:3302:5: note: in instantiation of member function 'std::basic_string::append' requested here 3302 | append(__n - __sz, __c); | ^ /usr/include/c++/v1/string:1303:84: note: in instantiation of member function 'std::basic_string::resize' requested here 1303 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 void resize(size_type __n) { resize(__n, value_type()); } | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/png_canvas.h:443:24: note: in instantiation of member function 'std::basic_string::resize' requested here 443 | idatChunk.data.resize(height + 4 * canvas.size()); // same as input, should be enough | ^ /usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: In file included from /usr/include/c++/v1/fstream:193: In file included from /usr/include/c++/v1/__locale:24: /usr/include/c++/v1/string:2538:5: error: implicit instantiation of undefined template 'std::char_traits' 2538 | traits_type::copy( | ^ /usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: In file included from /usr/include/c++/v1/fstream:193: In file included from /usr/include/c++/v1/__locale:24: /usr/include/c++/v1/string:2221:5: error: implicit instantiation of undefined template 'std::char_traits' 2221 | traits_type::assign(__p[__newsz], value_type()); | ^ /usr/include/c++/v1/string:2134:5: note: in instantiation of member function 'std::basic_string::__null_terminate_at' requested here 2134 | __null_terminate_at(std::__to_address(__get_pointer()), __pos); | ^ /usr/include/c++/v1/string:3304:5: note: in instantiation of member function 'std::basic_string::__erase_to_end' requested here 3304 | __erase_to_end(__n); | ^ /usr/include/c++/v1/string:1303:84: note: in instantiation of member function 'std::basic_string::resize' requested here 1303 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 void resize(size_type __n) { resize(__n, value_type()); } | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/png_canvas.h:443:24: note: in instantiation of member function 'std::basic_string::resize' requested here 443 | idatChunk.data.resize(height + 4 * canvas.size()); // same as input, should be enough | ^ /usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Roi_>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:432:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 432 | if (!open(roiFileIn, toCString(options.inputFileName))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ 19 warnings and 7 errors generated. [ 6% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 12 warnings generated. [ 7% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -MF apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o.d -o apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 17 warnings generated. [ 7% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o -MF apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o.d -o apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 17 warnings generated. [ 8% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o -MF apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o.d -o apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 20 warnings generated. [ 9% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -MF apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o.d -o apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 20 warnings generated. [ 9% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -MF apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o.d -o apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 20 warnings generated. [ 10% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -MF apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o.d -o apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 20 warnings generated. [ 11% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o -MF apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o.d -o apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:80:18: warning: variable 'i' set but not used [-Wunused-but-set-variable] 80 | unsigned i = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 21 warnings generated. [ 12% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -MF apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o.d -o apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:596:12: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::istream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 596 | return open(stream, fileStream, stream.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:651:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::istream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 651 | if (!open(file.stream, stream, compressionFormat)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:307:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, std::istream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>, seqan::True>' requested here 307 | _open(*this, istream, _mapFileFormatToCompressionFormat(format), True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:147:38: note: in instantiation of function template specialization 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 147 | bamFileIns.push_back(new seqan::BamFileIn(*outPtr, *splitter->files[i])); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_tangle.h:43:15: note: expanded from macro 'seqan' 43 | #define seqan seqan | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ 18 warnings generated. [ 12% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -MF apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o.d -o apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp FAILED: [code=1] apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -MF apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o.d -o apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:42: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:105:10: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 105 | std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/find_hamming_simple_ext.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment, seqan::PrefixSegment>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:471:12: note: in implicit copy constructor for 'seqan::Segment, seqan::PrefixSegment>' first required here 471 | return typename Prefix::Type(t, pos_end); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:341:48: note: in instantiation of function template specialization 'seqan::prefix, unsigned long>' requested here 341 | GsiRecord gsiRecord(CharString(prefix(readNameStore[readId], length(readNameStore[readId]) - 2)), flags, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:1231:5: note: in instantiation of function template specialization 'intervalizeAndDumpErrorCurves>>' requested here 1231 | intervalizeAndDumpErrorCurves(gsiStream, errorCurves, readAlignmentDistances, readNameStore, | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp 1. parser at end of file 2. Optimizer 3. Running pass "function(mem2reg,instcombine,simplifycfg)" on module "/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp" 4. Running pass "instcombine" on function "_ZN5seqan16getFileExtensionERKNS_16ArgParseArgumentEj" #0 0x000012f78ccb60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x000012f78ccb3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x000012f78cc643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x000012f7904e32dc (/lib/libthr.so.3+0x1a2dc) #4 0x000012f7904e28eb (/lib/libthr.so.3+0x198eb) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/rabema_build_gold_standard-3d010f.cpp c++: note: diagnostic msg: /tmp/rabema_build_gold_standard-3d010f.sh c++: note: diagnostic msg: ******************** [ 13% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -MF apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o.d -o apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'unary_function, char>' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::QualityExtractor>' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:491:67: note: in instantiation of template class 'seqan::ModifiedString>, seqan::ModView>>>' requested here 491 | ModifiedString > quals(seq); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:433:5: note: in instantiation of function template specialization 'seqan::writeRecord>, seqan::StreamIterator>>, seqan::String, seqan::String>>' requested here 433 | writeRecord(file.iter, meta, seq, Tag(), context(file).options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:471:9: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::String>, seqan::TagFastq_>' requested here 471 | writeRecord(file, meta, seq, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:479:5: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::Tag>, seqan::String, seqan::String>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here 479 | writeRecord(file, meta, seq, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:85:13: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::String>>' requested here 85 | writeRecord(stream, id, contig); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, char>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 19 warnings generated. [ 14% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -MF apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o.d -o apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp FAILED: [code=1] apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -MF apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o.d -o apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:33: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:596:12: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::istream, seqan::TagSelector>>>' requested here 596 | return open(stream, fileStream, stream.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:651:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::istream, seqan::TagSelector>>>' requested here 651 | if (!open(file.stream, stream, compressionFormat)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:267:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, std::istream, seqan::TagSelector>>, seqan::True>' requested here 267 | _open(*this, istream, _mapFileFormatToCompressionFormat(format), True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:264:15: note: in instantiation of function template specialization 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 264 | SeqFileIn reader(file); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:97:5: note: in instantiation of function template specialization 'seqan::qualityDistributionFromFastQFile>' requested here 97 | qualityDistributionFromFastQFile(ss, qualDist, pmOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:172:5: note: in instantiation of function template specialization 'SEQAN_TEST_test_param_chooser_quality_distribution_from_fastq_file' requested here 172 | SEQAN_CALL_TEST(test_param_chooser_quality_distribution_from_fastq_file); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:1701:13: note: expanded from macro 'SEQAN_CALL_TEST' 1701 | SEQAN_TEST_ ## test_name(); \ | ^ :32:1: note: expanded from here 32 | SEQAN_TEST_test_param_chooser_quality_distribution_from_fastq_file | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp 1. parser at end of file 2. Code generation 3. Running pass 'Function Pass Manager' on module '/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp'. 4. Running pass 'CodeGen Prepare' on function '@_ZN5seqan13AssertFunctorINS_9OrFunctorINS_10EqualsCharILc48EEENS2_ILc49EEEEENS_10ParseErrorENS_3TagINS_8Nothing_EEELb0EEclIcEEbRKT_' #0 0x00003817e10b60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x00003817e10b3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x00003817e10643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00003817e2e832dc (/lib/libthr.so.3+0x1a2dc) #4 0x00003817e2e828eb (/lib/libthr.so.3+0x198eb) #5 0x00003817d618f2d3 ([vdso]+0x2d3) #6 0x00003817dffd2cb4 (/usr/lib/libprivatellvm.so.19+0x27d2cb4) #7 0x00003817dffd114b (/usr/lib/libprivatellvm.so.19+0x27d114b) #8 0x00003817e0aa34c2 llvm::FPPassManager::runOnFunction(llvm::Function&) (/usr/lib/libprivatellvm.so.19+0x32a34c2) #9 0x00003817e0aa9104 llvm::FPPassManager::runOnModule(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a9104) #10 0x00003817e0aa3d13 llvm::legacy::PassManagerImpl::run(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a3d13) #11 0x00003817da26cce3 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr, std::__1::unique_ptr>, clang::BackendConsumer*) (/usr/lib/libprivateclang.so.19+0x226cce3) #12 0x00003817da60aef3 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/usr/lib/libprivateclang.so.19+0x260aef3) #13 0x00003817dac8fd29 clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fd29) #14 0x00003817dab21189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #15 0x00003817daa9e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #16 0x00003817daba779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #17 0x0000380fb4b3689e (/usr/bin/c+++0xd89e) #18 0x0000380fb4b43d53 (/usr/bin/c+++0x1ad53) #19 0x00003817da77d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #20 0x00003817e1064146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #21 0x00003817da77cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #22 0x00003817da740af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #23 0x00003817da740d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #24 0x00003817da75d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #25 0x0000380fb4b434c8 (/usr/bin/c+++0x1a4c8) #26 0x0000380fb4b41a92 (/usr/bin/c+++0x18a92) #27 0x00003817e44f837f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/test_param_chooser-1acaef.cpp c++: note: diagnostic msg: /tmp/test_param_chooser-1acaef.sh c++: note: diagnostic msg: ******************** [ 14% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -MF apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o.d -o apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: warning: definition of implicit copy assignment operator for 'IntervalTreeNode>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1441:18: note: in implicit copy assignment operator for 'seqan::IntervalTreeNode>' first required here 1441 | act_prop = property(pm, act_knot); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1502:5: note: in instantiation of function template specialization 'seqan::findIntervals>, seqan::String>>, int, GenomicInterval>' requested here 1502 | findIntervals(result, it.g, it.pm, query); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:718:5: note: in instantiation of function template specialization 'seqan::findIntervals' requested here 718 | findIntervals(intervals, svIntervalTree, svPos); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:88: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: 'binary_function, seqan::GapAnchor, bool>' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:327:9: note: in instantiation of template class 'seqan::_LessGapAnchor, const seqan::Tag>' requested here 327 | _LessGapAnchor::Type, SortSeqPos const>() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:848:25: note: in instantiation of function template specialization 'seqan::upperBoundGapAnchor>, int>' requested here 848 | anchorIdx = upperBoundGapAnchor(anchors, pos, SortSeqPos()) - begin(anchors, Standard()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:874:12: note: in instantiation of function template specialization 'seqan::positionSeqToGap, seqan::String>, int>' requested here 874 | return positionSeqToGap(gaps, sourcePosition) - gaps.data_viewCutBegin - gaps.data_cutBegin; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:803:21: note: in instantiation of function template specialization 'seqan::toViewPosition, seqan::String>, int>' requested here 803 | int beginPos2 = toViewPosition(refGaps, beginPos); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::GapAnchor, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:88: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: 'binary_function, seqan::GapAnchor, bool>' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:359:9: note: in instantiation of template class 'seqan::_LessGapAnchor, const seqan::Tag>' requested here 359 | _LessGapAnchor::Type, SortGapPos const>() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:758:25: note: in instantiation of function template specialization 'seqan::upperBoundGapAnchor>, int>' requested here 758 | anchorIdx = upperBoundGapAnchor(anchors, pos, SortGapPos()) - begin(anchors, Standard()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:889:12: note: in instantiation of function template specialization 'seqan::positionGapToSeq, seqan::String>, int, seqan::Tag>' requested here 889 | return positionGapToSeq(gaps, clippedViewPos + gaps.data_viewCutBegin + gaps.data_cutBegin, TProjectionDir()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:431:12: note: in instantiation of function template specialization 'seqan::toSourcePosition, seqan::String>, int, seqan::Tag>' requested here 431 | return toSourcePosition(gaps, clippedViewPos, RightOfViewPos()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:804:21: note: in instantiation of function template specialization 'seqan::toSourcePosition, seqan::AnchorGaps>>, int>' requested here 804 | int beginPos3 = toSourcePosition(smallVarGaps, beginPos2); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::GapAnchor, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 23 warnings generated. [ 15% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o -MF apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o.d -o apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:53: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 18 warnings generated. [ 16% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -MF apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o.d -o apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment, seqan::PrefixSegment>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:471:12: note: in implicit copy constructor for 'seqan::Segment, seqan::PrefixSegment>' first required here 471 | return typename Prefix::Type(t, pos_end); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_utils.h:125:12: note: in instantiation of function template specialization 'seqan::prefix, unsigned long>' requested here 125 | return prefix(lhs, rhsLen) == rhs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/vcf_io/read_vcf.h:141:18: note: in instantiation of function template specialization 'seqan::startsWith, char[6]>' requested here 141 | if (!startsWith(buffer, "CHROM")) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/vcf_io/vcf_file.h:198:5: note: in instantiation of function template specialization 'seqan::readHeader>, seqan::StreamIterator>>, seqan::StringSet>, seqan::NameStoreCache>>, seqan::Dependent<>>' requested here 198 | readHeader(header, context(file), file.iter, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:171:9: note: in instantiation of function template specialization 'seqan::readHeader' requested here 171 | readHeader(vcfHeader, vcfFileIn); | ^ 21 warnings generated. [ 17% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -MF apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o.d -o apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 290 | if (!open(seqFile, toCString(options.inFilename))) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 290 | if (!open(seqFile, toCString(options.inFilename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 290 | if (!open(seqFile, toCString(options.inFilename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 290 | if (!open(seqFile, toCString(options.inFilename))) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 290 | if (!open(seqFile, toCString(options.inFilename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 290 | if (!open(seqFile, toCString(options.inFilename))) | ^ 18 warnings generated. [ 17% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o -MF apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o.d -o apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 12 warnings generated. [ 18% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -MF apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o.d -o apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:254:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 254 | if (!open(bamFile, toCString(options.inBamPath))) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:254:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 254 | if (!open(bamFile, toCString(options.inBamPath))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:254:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 254 | if (!open(bamFile, toCString(options.inBamPath))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:254:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 254 | if (!open(bamFile, toCString(options.inBamPath))) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:254:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 254 | if (!open(bamFile, toCString(options.inBamPath))) | ^ 17 warnings generated. [ 19% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::Tag>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:5: note: in instantiation of function template specialization 'pairAlignConfig, seqan::Tag>' requested here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::Tag>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:5: note: in instantiation of function template specialization 'pairAlignConfig, seqan::Tag>' requested here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::Tag>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:5: note: in instantiation of function template specialization 'pairAlignConfig, seqan::Tag>' requested here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::Tag, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::Tag>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::Tag>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:5: note: in instantiation of function template specialization 'pairAlignConfig, seqan::Tag>' requested here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::Tag, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::Tag>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::Tag>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:5: note: in instantiation of function template specialization 'pairAlignConfig, seqan::Tag>' requested here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::Tag, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::Tag>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::Tag>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:5: note: in instantiation of function template specialization 'pairAlignConfig, seqan::Tag>' requested here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ^ 18 warnings generated. [ 19% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o -MF apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o.d -o apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 18 warnings generated. [ 20% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -MF apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o.d -o apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::QualityExtractor' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:491:67: note: in instantiation of template class 'seqan::ModifiedString, seqan::ModView>>' requested here 491 | ModifiedString > quals(seq); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:433:5: note: in instantiation of function template specialization 'seqan::writeRecord>, seqan::StreamIterator>>, const char *, seqan::String>' requested here 433 | writeRecord(file.iter, meta, seq, Tag(), context(file).options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:471:9: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::TagFastq_>' requested here 471 | writeRecord(file, meta, seq, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:479:5: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::Tag>, const char *, seqan::String, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here 479 | writeRecord(file, meta, seq, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:170:9: note: in instantiation of function template specialization 'seqan::writeRecord>' requested here 170 | writeRecord(outStream, ssTop.str().c_str(), levels.forward); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 21 warnings generated. [ 21% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o -MF apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o.d -o apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:596:12: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::istream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 596 | return open(stream, fileStream, stream.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:651:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::istream, seqan::Tag>' requested here 651 | if (!open(file.stream, stream, compressionFormat)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:267:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, std::istream, seqan::Tag, seqan::True>' requested here 267 | _open(*this, istream, _mapFileFormatToCompressionFormat(format), True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:151:9: note: in instantiation of function template specialization 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 151 | bedFileIn(inStream) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Bed_>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:657:10: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 657 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:267:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, std::istream, seqan::Tag, seqan::True>' requested here 267 | _open(*this, istream, _mapFileFormatToCompressionFormat(format), True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:151:9: note: in instantiation of function template specialization 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 151 | bedFileIn(inStream) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagGff_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:657:10: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 657 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:267:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, std::istream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>, seqan::True>' requested here 267 | _open(*this, istream, _mapFileFormatToCompressionFormat(format), True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:194:9: note: in instantiation of function template specialization 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 194 | gffFileIn(inStream), gffID(0), gffType(options.gffType) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagGtf_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:657:10: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 657 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:267:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, std::istream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>, seqan::True>' requested here 267 | _open(*this, istream, _mapFileFormatToCompressionFormat(format), True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:194:9: note: in instantiation of function template specialization 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 194 | gffFileIn(inStream), gffID(0), gffType(options.gffType) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Roi_>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:876:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 876 | if (!open(roiFileIn, toCString(options.inputRoiFile))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ 23 warnings generated. [ 21% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/bs_tools/CMakeFiles/four2three.dir/four2three.cpp.o -MF apps/bs_tools/CMakeFiles/four2three.dir/four2three.cpp.o.d -o apps/bs_tools/CMakeFiles/four2three.dir/four2three.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:40: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:14:34: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 14 | struct ConvertCT : public ::std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:40: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:23:34: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 23 | struct ConvertGA : public ::std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:41:23: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 41 | seqan::SeqFileIn seqFileIn(toCString(options.inputFileName)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:5: note: in instantiation of function template specialization 'preProcess' requested here 146 | preProcess(options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:596:12: note: (skipping 12 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 596 | return open(stream, fileStream, stream.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:231:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here 231 | readRecord(meta, seq, file, static_cast::Base const & >(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:231:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:296:5: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>>' requested here 296 | readRecord(meta, seq, file, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:52:13: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>' requested here 52 | readRecord(id, seq, seqFileIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:5: note: in instantiation of function template specialization 'preProcess' requested here 146 | preProcess(options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::QualityExtractor' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:491:67: note: in instantiation of template class 'seqan::ModifiedString, seqan::ModView>>' requested here 491 | ModifiedString > quals(seq); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:433:5: note: in instantiation of function template specialization 'seqan::writeRecord>, seqan::StreamIterator>>, seqan::String, seqan::String>' requested here 433 | writeRecord(file.iter, meta, seq, Tag(), context(file).options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:471:9: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::String, seqan::TagFastq_>' requested here 471 | writeRecord(file, meta, seq, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:479:5: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::Tag>, seqan::String, seqan::String, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here 479 | writeRecord(file, meta, seq, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:57:17: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::String>' requested here 57 | writeRecord(seqFileOut, id, tmp); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:5: note: in instantiation of function template specialization 'preProcess' requested here 146 | preProcess(options); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 23 warnings generated. [ 22% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -MF apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o.d -o apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 196 | seqan::SeqFileIn l(toCString(fileNameL)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:9: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 196 | seqan::SeqFileIn l(toCString(fileNameL)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:9: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 196 | seqan::SeqFileIn l(toCString(fileNameL)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:9: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 196 | seqan::SeqFileIn l(toCString(fileNameL)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:9: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 196 | seqan::SeqFileIn l(toCString(fileNameL)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:9: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 196 | seqan::SeqFileIn l(toCString(fileNameL)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:9: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment>, seqan::PrefixSegment>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:464:12: note: in implicit copy constructor for 'seqan::Segment>, seqan::PrefixSegment>' first required here 464 | return typename Prefix::Type(t, pos_end); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:289:22: note: in instantiation of function template specialization 'seqan::prefix>, unsigned long>' requested here 289 | append(seqL, prefix(seq, splitPos)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:443:9: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 443 | _importSequences(options.inPaths[0], seqs, mateSeqs, ids, sIds, quals, mateQuals); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment, seqan::PrefixSegment>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:464:12: note: in implicit copy constructor for 'seqan::Segment, seqan::PrefixSegment>' first required here 464 | return typename Prefix::Type(t, pos_end); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:295:27: note: in instantiation of function template specialization 'seqan::prefix, unsigned long>' requested here 295 | append(qualL, prefix(qual, splitPos)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:443:9: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 443 | _importSequences(options.inPaths[0], seqs, mateSeqs, ids, sIds, quals, mateQuals); | ^ 20 warnings generated. [ 23% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp FAILED: [code=1] apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp 1. parser at end of file 2. Optimizer 3. Running pass "require,function(invalidate),require,cgscc(devirt<4>(inline,function-attrs,openmp-opt-cgscc,function(sroa,early-cse,speculative-execution,jump-threading,correlated-propagation,simplifycfg,instcombine,aggressive-instcombine,libcalls-shrinkwrap,tailcallelim,simplifycfg,reassociate,constraint-elimination,loop-mssa(loop-instsimplify,loop-simplifycfg,licm,loop-rotate,licm,simple-loop-unswitch),simplifycfg,instcombine,loop(loop-idiom,indvars,simple-loop-unswitch,loop-deletion,loop-unroll-full),sroa,vector-combine,mldst-motion,gvn<>,sccp,bdce,instcombine,jump-threading,correlated-propagation,adce,memcpyopt,dse,move-auto-init,loop-mssa(licm),coro-elide,simplifycfg,instcombine),function-attrs,function(require),coro-split)),function(invalidate),cgscc(devirt<4>())" on module "/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp" 4. Running pass "cgscc(devirt<4>(inline,function-attrs,openmp-opt-cgscc,function(sroa,early-cse,speculative-execution,jump-threading,correlated-propagation,simplifycfg,instcombine,aggressive-instcombine,libcalls-shrinkwrap,tailcallelim,simplifycfg,reassociate,constraint-elimination,loop-mssa(loop-instsimplify,loop-simplifycfg,licm,loop-rotate,licm,simple-loop-unswitch),simplifycfg,instcombine,loop(loop-idiom,indvars,simple-loop-unswitch,loop-deletion,loop-unroll-full),sroa,vector-combine,mldst-motion,gvn<>,sccp,bdce,instcombine,jump-threading,correlated-propagation,adce,memcpyopt,dse,move-auto-init,loop-mssa(licm),coro-elide,simplifycfg,instcombine),function-attrs,function(require),coro-split))" on module "/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp" #0 0x00001a87bb2b60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x00001a87bb2b3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x00001a87bb2643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00001a87bd9ba2dc (/lib/libthr.so.3+0x1a2dc) #4 0x00001a87bd9b98eb (/lib/libthr.so.3+0x198eb) #5 0x00001a87b0d422d3 ([vdso]+0x2d3) #6 0x00001a87bc3129f9 std::__1::pair, llvm::detail::DenseSetEmpty, llvm::DenseMapInfo, void>, llvm::detail::DenseSetPair>, false>, bool> llvm::DenseMapBase, llvm::detail::DenseSetEmpty, llvm::DenseMapInfo, void>, llvm::detail::DenseSetPair>>, llvm::AssertingVH, llvm::detail::DenseSetEmpty, llvm::DenseMapInfo, void>, llvm::detail::DenseSetPair>>::try_emplace(llvm::AssertingVH const&, llvm::detail::DenseSetEmpty&) (/usr/lib/libprivatellvm.so.19+0x49129f9) #7 0x00001a87bc305ec6 llvm::SetVector, std::__1::deque, std::__1::allocator>>, llvm::DenseSet, llvm::DenseMapInfo, void>>, 0u>::insert(llvm::AssertingVH const&) (/usr/lib/libprivatellvm.so.19+0x4905ec6) #8 0x00001a87bacd9fba llvm::AnalysisManager::invalidate(llvm::Function&, llvm::PreservedAnalyses const&) (/usr/lib/libprivatellvm.so.19+0x32d9fba) #9 0x00001a87bbed643b llvm::InlinerPass::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x44d643b) #10 0x00001a87bb0944a2 llvm::detail::PassModel, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x36944a2) #11 0x00001a87b9d69151 llvm::PassManager, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x2369151) #12 0x00001a87bb080852 llvm::detail::PassModel, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>, llvm::AnalysisManager, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x3680852) #13 0x00001a87b9d6ae07 llvm::DevirtSCCRepeatedPass::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x236ae07) #14 0x00001a87bb0b2ba2 llvm::detail::PassModel, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x36b2ba2) #15 0x00001a87b9d6a59c llvm::ModuleToPostOrderCGSCCPassAdaptor::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x236a59c) #16 0x00001a87bb080a62 llvm::detail::PassModel>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x3680a62) #17 0x00001a87bacd8748 llvm::PassManager>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x32d8748) #18 0x00001a87bbed7417 llvm::ModuleInlinerWrapperPass::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x44d7417) #19 0x00001a87bb0890b2 llvm::detail::PassModel>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x36890b2) #20 0x00001a87bacd8748 llvm::PassManager>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x32d8748) #21 0x00001a87b4073899 (/usr/lib/libprivateclang.so.19+0x2273899) #22 0x00001a87b406c7f0 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr, std::__1::unique_ptr>, clang::BackendConsumer*) (/usr/lib/libprivateclang.so.19+0x226c7f0) #23 0x00001a87b440aef3 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/usr/lib/libprivateclang.so.19+0x260aef3) #24 0x00001a87b4a8fd29 clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fd29) #25 0x00001a87b4921189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #26 0x00001a87b489e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #27 0x00001a87b49a779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #28 0x00001a7f8f91189e (/usr/bin/c+++0xd89e) #29 0x00001a7f8f91ed53 (/usr/bin/c+++0x1ad53) #30 0x00001a87b457d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #31 0x00001a87bb264146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #32 0x00001a87b457cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #33 0x00001a87b4540af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #34 0x00001a87b4540d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #35 0x00001a87b455d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #36 0x00001a7f8f91e4c8 (/usr/bin/c+++0x1a4c8) #37 0x00001a7f8f91ca92 (/usr/bin/c+++0x18a92) #38 0x00001a87c079337f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/pair_align_global-c5e690.cpp c++: note: diagnostic msg: /tmp/pair_align_global-c5e690.sh c++: note: diagnostic msg: ******************** [ 24% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o -MF apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o.d -o apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp FAILED: [code=1] apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o -MF apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o.d -o apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_parse_options.h:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_out.h:46: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:161:19: warning: variable 'i' set but not used [-Wunused-but-set-variable] 161 | for (unsigned i = 0; !atEnd(leftMates) && !atEnd(rightMates); ++i, ++seqCount) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:25: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 143 | if (!open(leftMates, toCString(fileNameL))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:14: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 143 | if (!open(leftMates, toCString(fileNameL))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:14: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 143 | if (!open(leftMates, toCString(fileNameL))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:14: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 143 | if (!open(leftMates, toCString(fileNameL))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:14: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 143 | if (!open(leftMates, toCString(fileNameL))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:14: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:25: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 143 | if (!open(leftMates, toCString(fileNameL))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:14: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:24: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:86: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: warning: definition of implicit copy assignment operator for 'Iter>, seqan::CountingIteratorImpl_>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 105 | Iter(Iter const & other_) : | ^ /usr/include/c++/v1/__algorithm/sift_down.h:62:14: note: in implicit copy assignment operator for 'seqan::Iter>, seqan::CountingIteratorImpl_>>' first required here 62 | __start = __child_i; | ^ /usr/include/c++/v1/__algorithm/make_heap.h:39:12: note: in instantiation of function template specialization 'std::__sift_down> &, seqan::Iter>, seqan::CountingIteratorImpl_>>>' requested here 39 | std::__sift_down<_AlgPolicy>(__first, __comp_ref, __n, __first + __start); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:41:8: note: in instantiation of function template specialization 'std::__make_heap> &, seqan::Iter>, seqan::CountingIteratorImpl_>>>' requested here 41 | std::__make_heap<_AlgPolicy>(__first, __middle, __comp); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:65:12: note: in instantiation of function template specialization 'std::__partial_sort_impl> &, seqan::Iter>, seqan::CountingIteratorImpl_>>, seqan::Iter>, seqan::CountingIteratorImpl_>>>' requested here 65 | std::__partial_sort_impl<_AlgPolicy>(__first, __middle, __last, static_cast<__comp_ref_type<_Compare> >(__comp)); | ^ /usr/include/c++/v1/__algorithm/sort.h:992:10: note: in instantiation of function template specialization 'std::__partial_sort>, seqan::Iter>, seqan::CountingIteratorImpl_>>, seqan::Iter>, seqan::CountingIteratorImpl_>>>' requested here 992 | std::__partial_sort<_AlgPolicy>( | ^ /usr/include/c++/v1/__algorithm/sort.h:1003:8: note: in instantiation of function template specialization 'std::__sort_impl>, seqan::CountingIteratorImpl_>>, IdComparator>>' requested here 1003 | std::__sort_impl<_ClassicAlgPolicy>(std::move(__first), std::move(__last), __comp); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:196:10: note: in instantiation of function template specialization 'std::sort>, seqan::CountingIteratorImpl_>>, IdComparator>>' requested here 196 | std::sort(begin(uniqueIds, Standard()), end(uniqueIds, Standard()), IdComparator()); // O(n*log(n)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:14: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:24: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:86: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:71: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/iterator_counting.h:74:5: warning: definition of implicit copy assignment operator for 'Iter>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 74 | Iter(Iter const & other) : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:81:7: note: in implicit copy assignment operator for 'seqan::Iter>' first required here 81 | class Iter : | ^ /usr/include/c++/v1/__algorithm/sift_down.h:62:14: note: in implicit copy assignment operator for 'seqan::Iter>, seqan::CountingIteratorImpl_>>' first required here 62 | __start = __child_i; | ^ /usr/include/c++/v1/__algorithm/make_heap.h:39:12: note: in instantiation of function template specialization 'std::__sift_down> &, seqan::Iter>, seqan::CountingIteratorImpl_>>>' requested here 39 | std::__sift_down<_AlgPolicy>(__first, __comp_ref, __n, __first + __start); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:41:8: note: in instantiation of function template specialization 'std::__make_heap> &, seqan::Iter>, seqan::CountingIteratorImpl_>>>' requested here 41 | std::__make_heap<_AlgPolicy>(__first, __middle, __comp); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:65:12: note: in instantiation of function template specialization 'std::__partial_sort_impl> &, seqan::Iter>, seqan::CountingIteratorImpl_>>, seqan::Iter>, seqan::CountingIteratorImpl_>>>' requested here 65 | std::__partial_sort_impl<_AlgPolicy>(__first, __middle, __last, static_cast<__comp_ref_type<_Compare> >(__comp)); | ^ /usr/include/c++/v1/__algorithm/sort.h:992:10: note: in instantiation of function template specialization 'std::__partial_sort>, seqan::Iter>, seqan::CountingIteratorImpl_>>, seqan::Iter>, seqan::CountingIteratorImpl_>>>' requested here 992 | std::__partial_sort<_AlgPolicy>( | ^ /usr/include/c++/v1/__algorithm/sort.h:1003:8: note: in instantiation of function template specialization 'std::__sort_impl>, seqan::CountingIteratorImpl_>>, IdComparator>>' requested here 1003 | std::__sort_impl<_ClassicAlgPolicy>(std::move(__first), std::move(__last), __comp); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:196:10: note: in instantiation of function template specialization 'std::sort>, seqan::CountingIteratorImpl_>>, IdComparator>>' requested here 196 | std::sort(begin(uniqueIds, Standard()), end(uniqueIds, Standard()), IdComparator()); // O(n*log(n)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:14: note: in instantiation of function template specialization '_importSequences>, seqan::String>' requested here 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:188: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^ /usr/include/c++/v1/__type_traits/is_empty.h:22:71: note: in instantiation of template class 'seqan::RepeatLess_' requested here 22 | struct _LIBCPP_TEMPLATE_VIS is_empty : public integral_constant {}; | ^ /usr/include/c++/v1/map:627:18: note: in instantiation of template class 'std::is_empty>' requested here 627 | bool = is_empty<_Compare>::value && !__libcpp_is_final<_Compare>::value> | ^ /usr/include/c++/v1/map:994:11: note: in instantiation of default argument for '__map_value_compare' required here 994 | typedef __map_value_compare __vc; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:518:21: note: in instantiation of template class 'std::map, seqan::RepeatLess_>' requested here 518 | TRepeatList list; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:398:13: note: in instantiation of function template specialization 'seqan::findRepeats>, seqan::String>, unsigned int, unsigned int>' requested here 398 | findRepeats(data_repeats, haystack, minRepeatLen, maxPeriod); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:196:21: note: in instantiation of function template specialization 'seqan::Finder>, seqan::Swift>::Finder' requested here 196 | TFinder swiftFinder(databases[i], stellarOptions.minRepeatLength, stellarOptions.maxRepeatPeriod); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:9: note: in instantiation of function template specialization '_getStellarMatches>, seqan::StringSet>, seqan::String>>>>' requested here 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:131:9: warning: definition of implicit copy assignment operator for 'Index>, seqan::Dependent<>>, seqan::IndexQGram, seqan::Tag>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 131 | Index(Index &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index>, seqan::Dependent<>>, seqan::IndexQGram, seqan::Tag>>' first required here 110 | target = source; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign>, seqan::Dependent<>>, seqan::IndexQGram, seqan::Tag>>, seqan::Index>, seqan::Dependent<>>, seqan::IndexQGram, seqan::Tag>>>' requested here 645 | assign(_dataValue(me), value_); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create>, seqan::Dependent<>>, seqan::IndexQGram, seqan::Tag>>, seqan::Index>, seqan::Dependent<>>, seqan::IndexQGram, seqan::Tag>>>' requested here 594 | create(me, _dataValue(me)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create>, seqan::Dependent<>>, seqan::IndexQGram, seqan::Tag>>>' requested here 863 | create(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: in instantiation of function template specialization 'seqan::value>, seqan::Dependent<>>, seqan::IndexQGram, seqan::Tag>>>' requested here 339 | return value(me.data_host); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:740:37: note: in instantiation of function template specialization 'seqan::host>, seqan::Dependent<>>, seqan::IndexQGram, seqan::Tag>>, seqan::Swift>' requested here 740 | TSize seqCount = countSequences(host(pattern)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:9: note: in instantiation of function template specialization 'seqan::_patternInit>, seqan::Dependent<>>, seqan::IndexQGram, seqan::Tag>>, double, int, seqan::Tag>' requested here 1929 | _patternInit(pattern, errorRate, minLength); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:674:9: note: in instantiation of function template specialization 'seqan::find>, seqan::Index>, seqan::Dependent<>>, seqan::IndexQGram, seqan::Tag>>, seqan::Tag, int>' requested here 674 | while (find(finder, pattern, epsilon, minLength)) { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:13: note: in instantiation of function template specialization 'stellar>, seqan::Dependent<>, seqan::IndexQGram, seqan::Tag>, int, double, unsigned int, bool, seqan::String>, seqan::String, seqan::Tag>' requested here 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:9: note: in instantiation of function template specialization '_getStellarMatches>, seqan::StringSet>, seqan::String>>>>' requested here 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:24: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:86: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: warning: definition of implicit copy assignment operator for 'Iter, seqan::CountingIteratorImpl_>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 105 | Iter(Iter const & other_) : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: note: in implicit copy assignment operator for 'seqan::Iter, seqan::CountingIteratorImpl_>>' first required here 287 | matIt2 = matIt - diagonalWidth; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:5: note: in instantiation of function template specialization 'seqan::_alignBandedSmithWatermanDeclump>>>, seqan::Segment>>>, seqan::Score<>, int>' requested here 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:16: note: in instantiation of function template specialization 'seqan::_localAlignmentNext>>>, seqan::Tag, seqan::Segment>>>, seqan::Tag, seqan::Score<>, int>' requested here 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:12: note: in instantiation of function template specialization 'seqan::nextLocalAlignment, seqan::Segment>>>, seqan::Tag, seqan::Segment>>>, seqan::Tag>' requested here 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:607:12: note: in instantiation of function template specialization 'seqan::nextLocalAlignment, seqan::Segment>>>, seqan::Tag>' requested here 607 | while (nextLocalAlignment(localAlign, enumerator)) { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:3: note: in instantiation of function template specialization 'verifySwiftHit>>, double, int, unsigned int, double, unsigned int, seqan::String, seqan::String>, seqan::Tag>' requested here 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:13: note: in instantiation of function template specialization 'stellar>, seqan::Dependent<>, seqan::IndexQGram, seqan::Tag>, int, double, unsigned int, bool, seqan::String>, seqan::String, seqan::Tag>' requested here 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:9: note: in instantiation of function template specialization '_getStellarMatches>, seqan::StringSet>, seqan::String>>>>' requested here 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seeds.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:97: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: warning: definition of implicit copy constructor for 'Align>>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 104 | Align & operator=(Align const & other) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:194:24: note: in implicit copy constructor for 'seqan::Align>>>>' first required here 194 | TAlign ali(align); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:614:9: note: in instantiation of function template specialization '_splitAtXDrops>>>>, int, int, int>' requested here 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:3: note: in instantiation of function template specialization 'verifySwiftHit>>, double, int, unsigned int, double, unsigned int, seqan::String, seqan::String>, seqan::Tag>' requested here 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:13: note: in instantiation of function template specialization 'stellar>, seqan::Dependent<>, seqan::IndexQGram, seqan::Tag>, int, double, unsigned int, bool, seqan::String>, seqan::String, seqan::Tag>' requested here 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:9: note: in instantiation of function template specialization '_getStellarMatches>, seqan::StringSet>, seqan::String>>>>' requested here 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:24: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:98: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:57: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/triple_base.h:123:12: warning: definition of implicit copy assignment operator for 'Triple' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 123 | inline Triple(Triple const & _p) | ^ /usr/include/c++/v1/__algorithm/move.h:42:17: note: in implicit copy assignment operator for 'seqan::Triple' first required here 42 | *__result = _IterOps<_AlgPolicy>::__iter_move(__first); | ^ /usr/include/c++/v1/__algorithm/copy_move_common.h:95:19: note: in instantiation of function template specialization 'std::__move_impl::operator() *, seqan::Triple *, seqan::Triple *>' requested here 95 | auto __result = _Algorithm()(std::move(__range.first), std::move(__range.second), std::__unwrap_iter(__out_first)); | ^ /usr/include/c++/v1/__algorithm/move.h:110:15: note: in instantiation of function template specialization 'std::__copy_move_unwrap_iters, seqan::Triple *, seqan::Triple *, seqan::Triple *, 0>' requested here 110 | return std::__copy_move_unwrap_iters<__move_impl<_AlgPolicy> >( | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:760:10: note: in instantiation of function template specialization 'std::move *, seqan::Triple *>' requested here 760 | std::move(source_begin, source_end, target_begin); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1188:5: note: in instantiation of function template specialization 'seqan::_arrayMoveForwardDefault *, seqan::Triple *, seqan::Triple *>' requested here 1188 | _arrayMoveForwardDefault(source_begin, source_end, target_begin); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1197:5: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1197 | _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:182:14: note: in instantiation of function template specialization '_negativeMerge>' requested here 182 | if (!_negativeMerge(queue)) { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:614:9: note: in instantiation of function template specialization '_splitAtXDrops>>>>, int, int, int>' requested here 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:3: note: in instantiation of function template specialization 'verifySwiftHit>>, double, int, unsigned int, double, unsigned int, seqan::String, seqan::String>, seqan::Tag>' requested here 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:13: note: in instantiation of function template specialization 'stellar>, seqan::Dependent<>, seqan::IndexQGram, seqan::Tag>, int, double, unsigned int, bool, seqan::String>, seqan::String, seqan::Tag>' requested here 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:9: note: in instantiation of function template specialization '_getStellarMatches>, seqan::StringSet>, seqan::String>>>>' requested here 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:30: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_types.h:155:32: warning: 'binary_function>, seqan::String>, StellarMatch>, seqan::String>, bool>' is deprecated [-Wdeprecated-declarations] 155 | struct LessPos : public ::std::binary_function { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:307:23: note: in instantiation of template class 'LessPos>, seqan::String>>' requested here 307 | sortMatches(matches, LessPos()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:723:4: note: in instantiation of function template specialization 'maskOverlaps>, seqan::String, int>' requested here 723 | maskOverlaps(qm.matches, minLength); // remove overlaps and duplicates | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:13: note: in instantiation of function template specialization 'stellar>, seqan::Dependent<>, seqan::IndexQGram, seqan::Tag>, int, double, unsigned int, bool, seqan::String>, seqan::String, seqan::Tag>' requested here 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:9: note: in instantiation of function template specialization '_getStellarMatches>, seqan::StringSet>, seqan::String>>>>' requested here 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::String>, StellarMatch>, seqan::String>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:30: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_types.h:207:35: warning: 'binary_function>, seqan::String>, StellarMatch>, seqan::String>, bool>' is deprecated [-Wdeprecated-declarations] 207 | struct LessLength : public ::std::binary_function { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:370:23: note: in instantiation of template class 'LessLength>, seqan::String>>' requested here 370 | sortMatches(matches, LessLength()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:724:4: note: in instantiation of function template specialization 'compactMatches>, seqan::String, unsigned int>' requested here 724 | compactMatches(qm.matches, numMatches); // keep only the longest matches | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:13: note: in instantiation of function template specialization 'stellar>, seqan::Dependent<>, seqan::IndexQGram, seqan::Tag>, int, double, unsigned int, bool, seqan::String>, seqan::String, seqan::Tag>' requested here 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:9: note: in instantiation of function template specialization '_getStellarMatches>, seqan::StringSet>, seqan::String>>>>' requested here 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::String>, StellarMatch>, seqan::String>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seeds.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: warning: definition of implicit copy assignment operator for 'IntervalTreeNode>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1562:18: note: in implicit copy assignment operator for 'seqan::IntervalTreeNode>' first required here 1562 | act_prop = property(pm, act_knot); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1532:5: note: in instantiation of function template specialization 'seqan::findIntervals>, seqan::String>>, unsigned int, unsigned int, unsigned int>' requested here 1532 | findIntervals(result, g, pm, act_knot, query_begin, query_end); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1513:5: note: in instantiation of function template specialization 'seqan::findIntervals>, seqan::String>>, unsigned int, unsigned int>' requested here 1513 | findIntervals(result, tree.g, tree.pm, query_begin, query_end); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:255:5: note: in instantiation of function template specialization 'seqan::findIntervals' requested here 255 | findIntervals(confMateMatches, gustafChain.rightMateTree, mateIntervalBegin, mateIntervalEnd); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:294:20: note: in instantiation of function template specialization '_checkRightMateMatches>, seqan::String>, MSplazerChain>, unsigned int, seqan::String, SparsePropertyMap>, seqan::String>, unsigned int>, seqan::String>, seqan::String>>>>' requested here 294 | return _checkRightMateMatches(sMatch, queryMatches, gustafChain, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:458:18: note: in instantiation of function template specialization '_checkMateMatches>, seqan::String>, MSplazerChain>, unsigned int, seqan::String, SparsePropertyMap>, seqan::String>, unsigned int>, seqan::String>, seqan::String>>>>' requested here 458 | if (!_checkMateMatches(queryMatches.matches[i], queryMatches.matches, chain, options)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_algorithms.h:840:17: note: in instantiation of function template specialization '_initialiseGraphMatePairs>, seqan::String, MSplazerChain>, unsigned int, seqan::String, SparsePropertyMap>, seqan::String>, unsigned int>, seqan::String>, seqan::String>>>>' requested here 840 | _initialiseGraphMatePairs(stellarMatches[i], queryIds[i], chain, msplazerOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:230:5: note: in instantiation of function template specialization '_chainQueryMatches>, seqan::String, seqan::String, MSplazerChain>, unsigned int, seqan::String, SparsePropertyMap>, seqan::String>, unsigned int>, seqan::String>, seqan::String>>>>' requested here 230 | _chainQueryMatches(stellarMatches, distanceScores, queryChains, queryIDs, queries, readJoinPositions, msplazerOptions); | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp 1. parser at end of file 2. Optimizer 3. Running pass "require,function(invalidate),require,cgscc(devirt<4>(inline,function-attrs,openmp-opt-cgscc,function(sroa,early-cse,speculative-execution,jump-threading,correlated-propagation,simplifycfg,instcombine,aggressive-instcombine,libcalls-shrinkwrap,tailcallelim,simplifycfg,reassociate,constraint-elimination,loop-mssa(loop-instsimplify,loop-simplifycfg,licm,loop-rotate,licm,simple-loop-unswitch),simplifycfg,instcombine,loop(loop-idiom,indvars,simple-loop-unswitch,loop-deletion,loop-unroll-full),sroa,vector-combine,mldst-motion,gvn<>,sccp,bdce,instcombine,jump-threading,correlated-propagation,adce,memcpyopt,dse,move-auto-init,loop-mssa(licm),coro-elide,simplifycfg,instcombine),function-attrs,function(require),coro-split)),function(invalidate),cgscc(devirt<4>())" on module "/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp" 4. Running pass "cgscc(devirt<4>(inline,function-attrs,openmp-opt-cgscc,function(sroa,early-cse,speculative-execution,jump-threading,correlated-propagation,simplifycfg,instcombine,aggressive-instcombine,libcalls-shrinkwrap,tailcallelim,simplifycfg,reassociate,constraint-elimination,loop-mssa(loop-instsimplify,loop-simplifycfg,licm,loop-rotate,licm,simple-loop-unswitch),simplifycfg,instcombine,loop(loop-idiom,indvars,simple-loop-unswitch,loop-deletion,loop-unroll-full),sroa,vector-combine,mldst-motion,gvn<>,sccp,bdce,instcombine,jump-threading,correlated-propagation,adce,memcpyopt,dse,move-auto-init,loop-mssa(licm),coro-elide,simplifycfg,instcombine),function-attrs,function(require),coro-split))" on module "/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp" 5. Running pass "gvn<>" on function "_ZN5seqan10_readUntilINS_6StringINS_10SimpleTypeIhNS_5Dna5_EEENS_5AllocIvEEEENS_4IterINS_13VirtualStreamIcNS_3TagINS_6Input_EEENSt3__111char_traitsIcEEEENS_14StreamIteratorISC_EEEENS_9OrFunctorINS_10EqualsCharILc10EEENSL_ILc13EEEEENSK_INSK_INSK_INSL_ILc32EEENSL_ILc9EEEEESO_EENS_13AssertFunctorINS_12IsInAlphabetIS4_EENS_10ParseErrorENSA_INS_9TagFasta_EEELb0EEEEEcS4_EEvRT_RT0_RT1_RT2_PNS_5RangeIPT3_EEPNS19_IPT4_EE" #0 0x000014e4196b60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x000014e4196b3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x000014e4196643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x000014e41cd472dc (/lib/libthr.so.3+0x1a2dc) #4 0x000014e41cd468eb (/lib/libthr.so.3+0x198eb) #5 0x000014e4100f72d3 ([vdso]+0x2d3) #6 0x000014e41a7129f9 std::__1::pair, llvm::detail::DenseSetEmpty, llvm::DenseMapInfo, void>, llvm::detail::DenseSetPair>, false>, bool> llvm::DenseMapBase, llvm::detail::DenseSetEmpty, llvm::DenseMapInfo, void>, llvm::detail::DenseSetPair>>, llvm::AssertingVH, llvm::detail::DenseSetEmpty, llvm::DenseMapInfo, void>, llvm::detail::DenseSetPair>>::try_emplace(llvm::AssertingVH const&, llvm::detail::DenseSetEmpty&) (/usr/lib/libprivatellvm.so.19+0x49129f9) #7 0x000014e41a705ec6 llvm::SetVector, std::__1::deque, std::__1::allocator>>, llvm::DenseSet, llvm::DenseMapInfo, void>>, 0u>::insert(llvm::AssertingVH const&) (/usr/lib/libprivatellvm.so.19+0x4905ec6) #8 0x000014e4190d9fba llvm::AnalysisManager::invalidate(llvm::Function&, llvm::PreservedAnalyses const&) (/usr/lib/libprivatellvm.so.19+0x32d9fba) #9 0x000014e4190d96c6 llvm::PassManager>::run(llvm::Function&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x32d96c6) #10 0x000014e412c7c7b2 llvm::detail::PassModel>, llvm::AnalysisManager>::run(llvm::Function&, llvm::AnalysisManager&) (/usr/lib/libprivateclang.so.19+0x227c7b2) #11 0x000014e41816be51 llvm::CGSCCToFunctionPassAdaptor::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x236be51) #12 0x000014e4194b2832 llvm::detail::PassModel, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x36b2832) #13 0x000014e418169151 llvm::PassManager, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x2369151) #14 0x000014e419480852 llvm::detail::PassModel, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>, llvm::AnalysisManager, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x3680852) #15 0x000014e41816ae07 llvm::DevirtSCCRepeatedPass::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x236ae07) #16 0x000014e4194b2ba2 llvm::detail::PassModel, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x36b2ba2) #17 0x000014e41816a59c llvm::ModuleToPostOrderCGSCCPassAdaptor::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x236a59c) #18 0x000014e419480a62 llvm::detail::PassModel>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x3680a62) #19 0x000014e4190d8748 llvm::PassManager>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x32d8748) #20 0x000014e41a2d7417 llvm::ModuleInlinerWrapperPass::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x44d7417) #21 0x000014e4194890b2 llvm::detail::PassModel>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x36890b2) #22 0x000014e4190d8748 llvm::PassManager>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x32d8748) #23 0x000014e412c73899 (/usr/lib/libprivateclang.so.19+0x2273899) #24 0x000014e412c6c7f0 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr, std::__1::unique_ptr>, clang::BackendConsumer*) (/usr/lib/libprivateclang.so.19+0x226c7f0) #25 0x000014e41300aef3 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/usr/lib/libprivateclang.so.19+0x260aef3) #26 0x000014e41368fd29 clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fd29) #27 0x000014e413521189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #28 0x000014e41349e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #29 0x000014e4135a779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #30 0x000014dbee82589e (/usr/bin/c+++0xd89e) #31 0x000014dbee832d53 (/usr/bin/c+++0x1ad53) #32 0x000014e41317d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #33 0x000014e419664146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #34 0x000014e41317cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #35 0x000014e413140af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #36 0x000014e413140d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #37 0x000014e41315d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #38 0x000014dbee8324c8 (/usr/bin/c+++0x1a4c8) #39 0x000014dbee830a92 (/usr/bin/c+++0x18a92) #40 0x000014e41eb3937f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/gustaf-43d5a1.cpp c++: note: diagnostic msg: /tmp/gustaf-43d5a1.sh c++: note: diagnostic msg: ******************** [ 24% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o -MF apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o.d -o apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:33: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:36: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:7: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:596:12: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::istream, seqan::TagSelector>>>' requested here 596 | return open(stream, fileStream, stream.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:651:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::istream, seqan::TagSelector>>>' requested here 651 | if (!open(file.stream, stream, compressionFormat)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:267:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, std::istream, seqan::TagSelector>>, seqan::True>' requested here 267 | _open(*this, istream, _mapFileFormatToCompressionFormat(format), True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:264:15: note: in instantiation of function template specialization 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 264 | SeqFileIn reader(file); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:314:13: note: in instantiation of function template specialization 'seqan::qualityDistributionFromFastQFile>' requested here 314 | qualityDistributionFromFastQFile(filestrm, avg_act, pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1074:4: note: in instantiation of function template specialization 'seqan::getAvgFromPrbDirectory>' requested here 1074 | getAvgFromPrbDirectory(pm_options.fname[0],errorDistribution,pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:9: note: in instantiation of function template specialization 'seqan::chooseParams>' requested here 339 | chooseParams(r_options, pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:91: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:268:5: warning: definition of implicit copy assignment operator for 'Index>, seqan::Owner>>, seqan::IndexQGram>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 268 | Index(Index &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>' first required here 110 | target = source; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>>' requested here 645 | assign(_dataValue(me), value_); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>>' requested here 594 | create(me, _dataValue(me)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram>>>' requested here 863 | create(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: in instantiation of function template specialization 'seqan::value>, seqan::Owner>>, seqan::IndexQGram>>>' requested here 339 | return value(me.data_host); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1625:27: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1625 | TReadSet &readSet = host(host(swiftPattern)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape<>, seqan::Tag>>' requested here 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2239:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape<>, seqan::Tag>>' requested here 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:5: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, int, seqan::RazerSSpec>' requested here 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:3: note: in instantiation of function template specialization 'seqan::makeSelectedStatsFile>' requested here 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:9: note: in instantiation of function template specialization 'seqan::chooseParams>' requested here 339 | chooseParams(r_options, pm_options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:188: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^ /usr/include/c++/v1/__type_traits/is_empty.h:22:71: note: in instantiation of template class 'seqan::RepeatLess_' requested here 22 | struct _LIBCPP_TEMPLATE_VIS is_empty : public integral_constant {}; | ^ /usr/include/c++/v1/map:627:18: note: in instantiation of template class 'std::is_empty>' requested here 627 | bool = is_empty<_Compare>::value && !__libcpp_is_final<_Compare>::value> | ^ /usr/include/c++/v1/map:994:11: note: in instantiation of default argument for '__map_value_compare' required here 994 | typedef __map_value_compare __vc; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:518:21: note: in instantiation of template class 'std::map, seqan::RepeatLess_>' requested here 518 | TRepeatList list; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:398:13: note: in instantiation of function template specialization 'seqan::findRepeats>, seqan::String>, int, int>' requested here 398 | findRepeats(data_repeats, haystack, minRepeatLen, maxPeriod); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1626:15: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1626 | TSwiftFinder swiftFinder(genome, options.repeatLength, 1); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape<>, seqan::Tag>>' requested here 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2239:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape<>, seqan::Tag>>' requested here 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:5: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, int, seqan::RazerSSpec>' requested here 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:3: note: in instantiation of function template specialization 'seqan::makeSelectedStatsFile>' requested here 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:9: note: in instantiation of function template specialization 'seqan::chooseParams>' requested here 339 | chooseParams(r_options, pm_options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:704:40: warning: 'binary_function, seqan::ReadMatch, bool>' is deprecated [-Wdeprecated-declarations] 704 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:838:3: note: in instantiation of template class 'seqan::LessRNoGEndPos>' requested here 838 | LessRNoGEndPos()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1683:6: note: in instantiation of function template specialization 'seqan::maskDuplicates>>' requested here 1683 | maskDuplicates(matches); // overlapping parallelograms cause duplicates | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:4: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, int, seqan::RazerSSpec>' requested here 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape<>, seqan::Tag>>' requested here 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2239:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape<>, seqan::Tag>>' requested here 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:5: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, int, seqan::RazerSSpec>' requested here 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:3: note: in instantiation of function template specialization 'seqan::makeSelectedStatsFile>' requested here 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:9: note: in instantiation of function template specialization 'seqan::chooseParams>' requested here 339 | chooseParams(r_options, pm_options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::ReadMatch, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:676:37: warning: 'binary_function, seqan::ReadMatch, bool>' is deprecated [-Wdeprecated-declarations] 676 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:872:3: note: in instantiation of template class 'seqan::LessRNoGPos>' requested here 872 | LessRNoGPos()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1683:6: note: in instantiation of function template specialization 'seqan::maskDuplicates>>' requested here 1683 | maskDuplicates(matches); // overlapping parallelograms cause duplicates | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:4: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, int, seqan::RazerSSpec>' requested here 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape<>, seqan::Tag>>' requested here 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2239:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape<>, seqan::Tag>>' requested here 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:5: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, int, seqan::RazerSSpec>' requested here 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:3: note: in instantiation of function template specialization 'seqan::makeSelectedStatsFile>' requested here 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:9: note: in instantiation of function template specialization 'seqan::chooseParams>' requested here 339 | chooseParams(r_options, pm_options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::ReadMatch, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:730:36: warning: 'binary_function, seqan::ReadMatch, bool>' is deprecated [-Wdeprecated-declarations] 730 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:901:3: note: in instantiation of template class 'seqan::LessErrors>' requested here 901 | LessErrors()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1683:6: note: in instantiation of function template specialization 'seqan::maskDuplicates>>' requested here 1683 | maskDuplicates(matches); // overlapping parallelograms cause duplicates | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:4: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, int, seqan::RazerSSpec>' requested here 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape<>, seqan::Tag>>' requested here 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2239:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape<>, seqan::Tag>>' requested here 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:5: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, int, seqan::RazerSSpec>' requested here 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:3: note: in instantiation of function template specialization 'seqan::makeSelectedStatsFile>' requested here 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:9: note: in instantiation of function template specialization 'seqan::chooseParams>' requested here 339 | chooseParams(r_options, pm_options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::ReadMatch, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:91: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:268:5: warning: definition of implicit copy assignment operator for 'Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 268 | Index(Index &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>' first required here 110 | target = source; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 645 | assign(_dataValue(me), value_); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 594 | create(me, _dataValue(me)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 863 | create(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: in instantiation of function template specialization 'seqan::value>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 339 | return value(me.data_host); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1625:27: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1625 | TReadSet &readSet = host(host(swiftPattern)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape, seqan::OneGappedShape>, seqan::Tag>>' requested here 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2242:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape, seqan::OneGappedShape>, seqan::Tag>>' requested here 2242 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:5: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, int, seqan::RazerSSpec>' requested here 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:3: note: in instantiation of function template specialization 'seqan::makeSelectedStatsFile>' requested here 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:9: note: in instantiation of function template specialization 'seqan::chooseParams>' requested here 339 | chooseParams(r_options, pm_options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:87: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: warning: definition of implicit copy assignment operator for 'Shape, seqan::OneGappedShape>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 107 | Shape(Shape const &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:52:57: note: in implicit copy assignment operator for 'seqan::Shape, seqan::OneGappedShape>' first required here 52 | template < typename TObject, typename TSpec > class Index; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>' first required here 110 | target = source; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 645 | assign(_dataValue(me), value_); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 594 | create(me, _dataValue(me)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 863 | create(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 339 | return value(me.data_host); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape, seqan::OneGappedShape>, seqan::Tag>>' requested here 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2242:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape, seqan::OneGappedShape>, seqan::Tag>>' requested here 2242 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:5: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, int, seqan::RazerSSpec>' requested here 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:3: note: in instantiation of function template specialization 'seqan::makeSelectedStatsFile>' requested here 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:9: note: in instantiation of function template specialization 'seqan::chooseParams>' requested here 339 | chooseParams(r_options, pm_options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:91: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:268:5: warning: definition of implicit copy assignment operator for 'Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 268 | Index(Index &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>' first required here 110 | target = source; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 645 | assign(_dataValue(me), value_); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 594 | create(me, _dataValue(me)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 863 | create(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: in instantiation of function template specialization 'seqan::value>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 339 | return value(me.data_host); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1625:27: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1625 | TReadSet &readSet = host(host(swiftPattern)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape, seqan::GappedShape>>, seqan::Tag>>' requested here 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2245:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape, seqan::GappedShape>>, seqan::Tag>>' requested here 2245 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:5: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, int, seqan::RazerSSpec>' requested here 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:3: note: in instantiation of function template specialization 'seqan::makeSelectedStatsFile>' requested here 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:9: note: in instantiation of function template specialization 'seqan::chooseParams>' requested here 339 | chooseParams(r_options, pm_options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: warning: definition of implicit copy assignment operator for 'Shape, seqan::GappedShape>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 281 | Shape(Shape const &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:52:57: note: in implicit copy assignment operator for 'seqan::Shape, seqan::GappedShape>>' first required here 52 | template < typename TObject, typename TSpec > class Index; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>' first required here 110 | target = source; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 645 | assign(_dataValue(me), value_); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 594 | create(me, _dataValue(me)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 863 | create(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 339 | return value(me.data_host); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape, seqan::GappedShape>>, seqan::Tag>>' requested here 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2245:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, seqan::RazerSSpec, seqan::Shape, seqan::GappedShape>>, seqan::Tag>>' requested here 2245 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:5: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>>, seqan::StringSet>, seqan::Owner>>, int, int, seqan::RazerSSpec>' requested here 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:3: note: in instantiation of function template specialization 'seqan::makeSelectedStatsFile>' requested here 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:9: note: in instantiation of function template specialization 'seqan::chooseParams>' requested here 339 | chooseParams(r_options, pm_options); | ^ 29 warnings generated. [ 25% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -MF apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o.d -o apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp FAILED: [code=1] apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -MF apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o.d -o apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:31: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:501:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 501 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename' requested here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1342:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 1342 | if (!open(inGsi, toCString(options.inGsiPath))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1342:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 1342 | if (!open(inGsi, toCString(options.inGsiPath))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: warning: definition of implicit copy assignment operator for 'IntervalTreeNode>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1441:18: note: in implicit copy assignment operator for 'seqan::IntervalTreeNode>' first required here 1441 | act_prop = property(pm, act_knot); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1502:5: note: in instantiation of function template specialization 'seqan::findIntervals>, seqan::String>>, unsigned int, unsigned int>' requested here 1502 | findIntervals(result, it.g, it.pm, query); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:644:9: note: in instantiation of function template specialization 'seqan::findIntervals' requested here 644 | findIntervals(queryResult, intervalTrees[seqId], lastPos); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1003:23: note: in instantiation of function template specialization 'benchmarkReadResult>' requested here 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1401:15: note: in instantiation of function template specialization 'compareAlignedReadsToReference>, seqan::StreamIterator>>, seqan::Tag>' requested here 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp 1. parser at end of file 2. Optimizer 3. Running pass "require,function(invalidate),require,cgscc(devirt<4>(inline,function-attrs,openmp-opt-cgscc,function(sroa,early-cse,speculative-execution,jump-threading,correlated-propagation,simplifycfg,instcombine,aggressive-instcombine,libcalls-shrinkwrap,tailcallelim,simplifycfg,reassociate,constraint-elimination,loop-mssa(loop-instsimplify,loop-simplifycfg,licm,loop-rotate,licm,simple-loop-unswitch),simplifycfg,instcombine,loop(loop-idiom,indvars,simple-loop-unswitch,loop-deletion,loop-unroll-full),sroa,vector-combine,mldst-motion,gvn<>,sccp,bdce,instcombine,jump-threading,correlated-propagation,adce,memcpyopt,dse,move-auto-init,loop-mssa(licm),coro-elide,simplifycfg,instcombine),function-attrs,function(require),coro-split)),function(invalidate),cgscc(devirt<4>())" on module "/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp" 4. Running pass "cgscc(devirt<4>(inline,function-attrs,openmp-opt-cgscc,function(sroa,early-cse,speculative-execution,jump-threading,correlated-propagation,simplifycfg,instcombine,aggressive-instcombine,libcalls-shrinkwrap,tailcallelim,simplifycfg,reassociate,constraint-elimination,loop-mssa(loop-instsimplify,loop-simplifycfg,licm,loop-rotate,licm,simple-loop-unswitch),simplifycfg,instcombine,loop(loop-idiom,indvars,simple-loop-unswitch,loop-deletion,loop-unroll-full),sroa,vector-combine,mldst-motion,gvn<>,sccp,bdce,instcombine,jump-threading,correlated-propagation,adce,memcpyopt,dse,move-auto-init,loop-mssa(licm),coro-elide,simplifycfg,instcombine),function-attrs,function(require),coro-split))" on module "/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp" 5. Running pass "loop-mssa(loop-instsimplify,loop-simplifycfg,licm,loop-rotate,licm,simple-loop-unswitch)" on function "_ZNSt3__111__make_heapB8se190107INS_17_ClassicAlgPolicyERPFbRKN5seqan13PointAndCargoIjjEES6_ENS2_4IterINS2_6StringIS4_NS2_5AllocIvEEEENS2_15AdaptorIteratorIPS4_NS2_3TagINS2_8Default_EEEEEEEEEvT1_SM_OT0_" 6. Running pass "loop-simplify" on function "_ZNSt3__111__make_heapB8se190107INS_17_ClassicAlgPolicyERPFbRKN5seqan13PointAndCargoIjjEES6_ENS2_4IterINS2_6StringIS4_NS2_5AllocIvEEEENS2_15AdaptorIteratorIPS4_NS2_3TagINS2_8Default_EEEEEEEEEvT1_SM_OT0_" #0 0x00000ef3898b60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x00000ef3898b3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x00000ef3898643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00000ef38db3b2dc (/lib/libthr.so.3+0x1a2dc) #4 0x00000ef38db3a8eb (/lib/libthr.so.3+0x198eb) #5 0x00000ef37f9252d3 ([vdso]+0x2d3) #6 0x00000ef38a9129f9 std::__1::pair, llvm::detail::DenseSetEmpty, llvm::DenseMapInfo, void>, llvm::detail::DenseSetPair>, false>, bool> llvm::DenseMapBase, llvm::detail::DenseSetEmpty, llvm::DenseMapInfo, void>, llvm::detail::DenseSetPair>>, llvm::AssertingVH, llvm::detail::DenseSetEmpty, llvm::DenseMapInfo, void>, llvm::detail::DenseSetPair>>::try_emplace(llvm::AssertingVH const&, llvm::detail::DenseSetEmpty&) (/usr/lib/libprivatellvm.so.19+0x49129f9) #7 0x00000ef38a905ec6 llvm::SetVector, std::__1::deque, std::__1::allocator>>, llvm::DenseSet, llvm::DenseMapInfo, void>>, 0u>::insert(llvm::AssertingVH const&) (/usr/lib/libprivatellvm.so.19+0x4905ec6) #8 0x00000ef3892d9fba llvm::AnalysisManager::invalidate(llvm::Function&, llvm::PreservedAnalyses const&) (/usr/lib/libprivatellvm.so.19+0x32d9fba) #9 0x00000ef3892d96c6 llvm::PassManager>::run(llvm::Function&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x32d96c6) #10 0x00000ef38a87549f llvm::FunctionToLoopPassAdaptor::run(llvm::Function&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x487549f) #11 0x00000ef3896af9c2 llvm::detail::PassModel>::run(llvm::Function&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x36af9c2) #12 0x00000ef3892d96b8 llvm::PassManager>::run(llvm::Function&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x32d96b8) #13 0x00000ef38307c7b2 llvm::detail::PassModel>, llvm::AnalysisManager>::run(llvm::Function&, llvm::AnalysisManager&) (/usr/lib/libprivateclang.so.19+0x227c7b2) #14 0x00000ef38836be51 llvm::CGSCCToFunctionPassAdaptor::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x236be51) #15 0x00000ef3896b2832 llvm::detail::PassModel, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x36b2832) #16 0x00000ef388369151 llvm::PassManager, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x2369151) #17 0x00000ef389680852 llvm::detail::PassModel, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>, llvm::AnalysisManager, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x3680852) #18 0x00000ef38836ae07 llvm::DevirtSCCRepeatedPass::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x236ae07) #19 0x00000ef3896b2ba2 llvm::detail::PassModel, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&>::run(llvm::LazyCallGraph::SCC&, llvm::AnalysisManager&, llvm::LazyCallGraph&, llvm::CGSCCUpdateResult&) (/usr/lib/libprivatellvm.so.19+0x36b2ba2) #20 0x00000ef38836a59c llvm::ModuleToPostOrderCGSCCPassAdaptor::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x236a59c) #21 0x00000ef389680a62 llvm::detail::PassModel>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x3680a62) #22 0x00000ef3892d8748 llvm::PassManager>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x32d8748) #23 0x00000ef38a4d7417 llvm::ModuleInlinerWrapperPass::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x44d7417) #24 0x00000ef3896890b2 llvm::detail::PassModel>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x36890b2) #25 0x00000ef3892d8748 llvm::PassManager>::run(llvm::Module&, llvm::AnalysisManager&) (/usr/lib/libprivatellvm.so.19+0x32d8748) #26 0x00000ef383073899 (/usr/lib/libprivateclang.so.19+0x2273899) #27 0x00000ef38306c7f0 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr, std::__1::unique_ptr>, clang::BackendConsumer*) (/usr/lib/libprivateclang.so.19+0x226c7f0) #28 0x00000ef38340aef3 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/usr/lib/libprivateclang.so.19+0x260aef3) #29 0x00000ef383a8fd29 clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fd29) #30 0x00000ef383921189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #31 0x00000ef38389e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #32 0x00000ef3839a779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #33 0x00000eeb5dad389e (/usr/bin/c+++0xd89e) #34 0x00000eeb5dae0d53 (/usr/bin/c+++0x1ad53) #35 0x00000ef38357d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #36 0x00000ef389864146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #37 0x00000ef38357cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #38 0x00000ef383540af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #39 0x00000ef383540d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #40 0x00000ef38355d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #41 0x00000eeb5dae04c8 (/usr/bin/c+++0x1a4c8) #42 0x00000eeb5dadea92 (/usr/bin/c+++0x18a92) #43 0x00000ef38fc6437f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/rabema_evaluate-9f5771.cpp c++: note: diagnostic msg: /tmp/rabema_evaluate-9f5771.sh c++: note: diagnostic msg: ******************** [ 26% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -MF apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o.d -o apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'unary_function, char>' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::QualityExtractor>' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:491:67: note: in instantiation of template class 'seqan::ModifiedString>, seqan::ModView>>>' requested here 491 | ModifiedString > quals(seq); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:433:5: note: in instantiation of function template specialization 'seqan::writeRecord>, seqan::StreamIterator>>, std::string, seqan::String>>' requested here 433 | writeRecord(file.iter, meta, seq, Tag(), context(file).options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:471:9: note: in instantiation of function template specialization 'seqan::writeRecord>, seqan::TagFastq_>' requested here 471 | writeRecord(file, meta, seq, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:479:5: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::Tag>, std::string, seqan::String>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here 479 | writeRecord(file, meta, seq, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:146:17: note: in instantiation of function template specialization 'seqan::writeRecord>>' requested here 146 | writeRecord(outStream, ssName.str(), seq); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, char>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::QualityExtractor' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:491:67: note: in instantiation of template class 'seqan::ModifiedString, seqan::ModView>>' requested here 491 | ModifiedString > quals(seq); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:433:5: note: in instantiation of function template specialization 'seqan::writeRecord>, seqan::StreamIterator>>, std::string, seqan::String>' requested here 433 | writeRecord(file.iter, meta, seq, Tag(), context(file).options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:471:9: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::TagFastq_>' requested here 471 | writeRecord(file, meta, seq, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:479:5: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::Tag>, std::string, seqan::String, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here 479 | writeRecord(file, meta, seq, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:155:17: note: in instantiation of function template specialization 'seqan::writeRecord>' requested here 155 | writeRecord(outMethLevelStream, ssTop.str(), levels.forward); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 22 warnings generated. [ 26% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o -MF apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o.d -o apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp FAILED: [code=1] apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o -MF apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o.d -o apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:27: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:268:34: warning: 'binary_function, SubstringEntry, bool>' is deprecated [-Wdeprecated-declarations] 268 | struct LessSubstringEnd : public binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:563:62: note: in instantiation of template class 'LessSubstringEnd>' requested here 563 | sort(begin(matches, Standard()), end(matches, Standard()), LessSubstringEnd()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:20: note: in instantiation of function template specialization 'runDFI, seqan::String, std::vector>' requested here 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, SubstringEntry, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:292:27: warning: 'binary_function, SubstringEntry, bool>' is deprecated [-Wdeprecated-declarations] 292 | struct LessRange : public binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:565:62: note: in instantiation of template class 'LessRange>' requested here 565 | sort(begin(matches, Standard()), end(matches, Standard()), LessRange()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:20: note: in instantiation of function template specialization 'runDFI, seqan::String, std::vector>' requested here 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, SubstringEntry, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:309:25: warning: 'binary_function, SubstringEntry, bool>' is deprecated [-Wdeprecated-declarations] 309 | struct LessLex : public binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:569:62: note: in instantiation of template class 'LessLex>' requested here 569 | sort(begin(matches, Standard()), end(matches, Standard()), LessLex()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:20: note: in instantiation of function template specialization 'runDFI, seqan::String, std::vector>' requested here 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, SubstringEntry, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:8: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 248 | if (!open(seqFile, toCString(fileNames[s]))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:7: note: in instantiation of function template specialization 'loadDatasets>, std::vector, seqan::String>' requested here 498 | if (!loadDatasets(mySet, fileNames, ds)) { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:20: note: in instantiation of function template specialization 'runDFI, seqan::String, std::vector>' requested here 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:8: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 248 | if (!open(seqFile, toCString(fileNames[s]))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:7: note: in instantiation of function template specialization 'loadDatasets>, std::vector, seqan::String>' requested here 498 | if (!loadDatasets(mySet, fileNames, ds)) { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:20: note: in instantiation of function template specialization 'runDFI, seqan::String, std::vector>' requested here 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:8: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 248 | if (!open(seqFile, toCString(fileNames[s]))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:7: note: in instantiation of function template specialization 'loadDatasets>, std::vector, seqan::String>' requested here 498 | if (!loadDatasets(mySet, fileNames, ds)) { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:20: note: in instantiation of function template specialization 'runDFI, seqan::String, std::vector>' requested here 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:8: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 248 | if (!open(seqFile, toCString(fileNames[s]))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:7: note: in instantiation of function template specialization 'loadDatasets>, std::vector, seqan::String>' requested here 498 | if (!loadDatasets(mySet, fileNames, ds)) { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:20: note: in instantiation of function template specialization 'runDFI, seqan::String, std::vector>' requested here 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:8: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 248 | if (!open(seqFile, toCString(fileNames[s]))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:7: note: in instantiation of function template specialization 'loadDatasets>, std::vector, seqan::String>' requested here 498 | if (!loadDatasets(mySet, fileNames, ds)) { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:20: note: in instantiation of function template specialization 'runDFI, seqan::String, std::vector>' requested here 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:8: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 248 | if (!open(seqFile, toCString(fileNames[s]))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:7: note: in instantiation of function template specialization 'loadDatasets>, std::vector, seqan::String>' requested here 498 | if (!loadDatasets(mySet, fileNames, ds)) { | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:20: note: in instantiation of function template specialization 'runDFI, seqan::String, std::vector>' requested here 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"2.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp 1. parser at end of file 2. Code generation 3. Running pass 'Function Pass Manager' on module '/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp'. 4. Running pass 'Loop Pass Manager' on function '@_ZN5seqan25_getCompressionExtensionsINSt3__16vectorINS1_12basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEENS6_IS8_EEEENS_4Sam_ENS_7TagListINS_3TagINS_8Nothing_EEEvEEEEvRT_RKNSD_IT0_EERKT1_bSF_' 5. Running pass 'Loop Strength Reduction' on basic block '%33' #0 0x000032a5364b60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x000032a5364b3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x000032a5364643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x000032a52d5b22dc (/lib/libthr.so.3+0x1a2dc) #4 0x000032a52d5b18eb (/lib/libthr.so.3+0x198eb) #5 0x000032a52d4a12d3 ([vdso]+0x2d3) #6 0x000032a53c1dc8fd (/lib/libc.so.7+0x18c8fd) #7 0x000032a53c1d396d (/lib/libc.so.7+0x18396d) #8 0x000032a535079fc2 std::__1::pair, llvm::detail::DenseSetPair, false>, bool> llvm::DenseMapBase, llvm::detail::DenseSetPair>, llvm::Type*, llvm::detail::DenseSetEmpty, llvm::DenseMapInfo, llvm::detail::DenseSetPair>::try_emplace(llvm::Type* const&, llvm::detail::DenseSetEmpty&) (/usr/lib/libprivatellvm.so.19+0x2479fc2) #9 0x000032a53749a48f llvm::SetVector, llvm::DenseSet>, 4u>::insert(llvm::Type* const&) (/usr/lib/libprivatellvm.so.19+0x489a48f) #10 0x000032a537488897 (/usr/lib/libprivatellvm.so.19+0x4888897) #11 0x000032a537484d47 (/usr/lib/libprivatellvm.so.19+0x4884d47) #12 0x000032a5374a7b35 (/usr/lib/libprivatellvm.so.19+0x48a7b35) #13 0x000032a53509a7ee llvm::LPPassManager::runOnFunction(llvm::Function&) (/usr/lib/libprivatellvm.so.19+0x249a7ee) #14 0x000032a535ea34c2 llvm::FPPassManager::runOnFunction(llvm::Function&) (/usr/lib/libprivatellvm.so.19+0x32a34c2) #15 0x000032a535ea9104 llvm::FPPassManager::runOnModule(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a9104) #16 0x000032a535ea3d13 llvm::legacy::PassManagerImpl::run(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a3d13) #17 0x000032a530a6cce3 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr, std::__1::unique_ptr>, clang::BackendConsumer*) (/usr/lib/libprivateclang.so.19+0x226cce3) #18 0x000032a530e0aef3 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/usr/lib/libprivateclang.so.19+0x260aef3) #19 0x000032a53148fd29 clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fd29) #20 0x000032a531321189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #21 0x000032a53129e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #22 0x000032a5313a779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #23 0x0000329d0bbac89e (/usr/bin/c+++0xd89e) #24 0x0000329d0bbb9d53 (/usr/bin/c+++0x1ad53) #25 0x000032a530f7d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #26 0x000032a536464146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #27 0x000032a530f7cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #28 0x000032a530f40af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #29 0x000032a530f40d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #30 0x000032a530f5d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #31 0x0000329d0bbb94c8 (/usr/bin/c+++0x1a4c8) #32 0x0000329d0bbb7a92 (/usr/bin/c+++0x18a92) #33 0x000032a53c0e137f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/dfi-e76694.cpp c++: note: diagnostic msg: /tmp/dfi-e76694.sh c++: note: diagnostic msg: ******************** [ 27% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/alf/CMakeFiles/alf.dir/alf.cpp.o -MF apps/alf/CMakeFiles/alf.dir/alf.cpp.o.d -o apps/alf/CMakeFiles/alf.dir/alf.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/statistics.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/statistics.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free.h:55: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free/kmer_functions.h:864:9: warning: variable 'counterN' set but not used [-Wunused-but-set-variable] 864 | int counterN = 0; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free/kmer_functions.h:943:9: warning: variable 'counterN' set but not used [-Wunused-but-set-variable] 943 | int counterN = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:9: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 164 | open(seqFile, toCString(inFile)); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:9: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 164 | open(seqFile, toCString(inFile)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:9: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 164 | open(seqFile, toCString(inFile)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:9: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 164 | open(seqFile, toCString(inFile)); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:9: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 164 | open(seqFile, toCString(inFile)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:9: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 164 | open(seqFile, toCString(inFile)); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:86: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: warning: definition of implicit copy assignment operator for 'Iter>, seqan::CountingIteratorImpl_>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 105 | Iter(Iter const & other_) : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free/af_n2.h:189:34: note: in implicit copy assignment operator for 'seqan::Iter>, seqan::CountingIteratorImpl_>>' first required here 189 | itStandardisedKmerCounts = begin(standardisedKmerCounts); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free/alignment_free_comparison.h:101:5: note: in instantiation of function template specialization 'seqan::_alignmentFreeComparison>>>' requested here 101 | _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:188:9: note: in instantiation of function template specialization 'seqan::alignmentFreeComparison>>, double, seqan::AFScore>' requested here 188 | alignmentFreeComparison(myMatrix, mySequenceSet, myScoreN2); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:86: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:71: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/iterator_counting.h:74:5: warning: definition of implicit copy assignment operator for 'Iter>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 74 | Iter(Iter const & other) : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:81:7: note: in implicit copy assignment operator for 'seqan::Iter>' first required here 81 | class Iter : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free/af_n2.h:189:34: note: in implicit copy assignment operator for 'seqan::Iter>, seqan::CountingIteratorImpl_>>' first required here 189 | itStandardisedKmerCounts = begin(standardisedKmerCounts); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free/alignment_free_comparison.h:101:5: note: in instantiation of function template specialization 'seqan::_alignmentFreeComparison>>>' requested here 101 | _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:188:9: note: in instantiation of function template specialization 'seqan::alignmentFreeComparison>>, double, seqan::AFScore>' requested here 188 | alignmentFreeComparison(myMatrix, mySequenceSet, myScoreN2); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment>, seqan::PrefixSegment>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:471:12: note: in implicit copy constructor for 'seqan::Segment>, seqan::PrefixSegment>' first required here 471 | return typename Prefix::Type(t, pos_end); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free/kmer_functions.h:723:39: note: in instantiation of function template specialization 'seqan::prefix>, unsigned long>' requested here 723 | String my_prefix = prefix(word2, my_min); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free/kmer_functions.h:593:5: note: in instantiation of function template specialization 'seqan::calculatePeriodicity>>' requested here 593 | calculatePeriodicity(periodicity1, word1, word2); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free/af_n2.h:395:29: note: in instantiation of function template specialization 'seqan::calculateCovariance>, seqan::String>' requested here 395 | calculateCovariance(value(covarianceMatrix, wordColHash, wordRowHash), wMM1, wMM2, backgroundFrequencies, (len1 + score.kmerSize - 1)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free/af_n2.h:179:9: note: in instantiation of function template specialization 'seqan::_standardiseCounts, seqan::String>>' requested here 179 | _standardiseCounts(*itStandardisedKmerCounts, revComIndex, kmerNeighbourhood, *itSeqSet, score); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/alignment_free/alignment_free_comparison.h:101:5: note: in instantiation of function template specialization 'seqan::_alignmentFreeComparison>>>' requested here 101 | _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:188:9: note: in instantiation of function template specialization 'seqan::alignmentFreeComparison>>, double, seqan::AFScore>' requested here 188 | alignmentFreeComparison(myMatrix, mySequenceSet, myScoreN2); | ^ 25 warnings generated. [ 28% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -MF apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o.d -o apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:31: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 18 warnings generated. [ 29% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -MF apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o.d -o apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:142:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 142 | if (!open(inFragments, toCString(options.inputFileName))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:596:12: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 596 | return open(stream, fileStream, stream.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:231:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here 231 | readRecord(meta, seq, file, static_cast::Base const & >(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:231:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:231:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:296:5: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>>' requested here 296 | readRecord(meta, seq, file, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:213:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>>' requested here 213 | readRecord(fragId, fragSeq, inFragments); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ 22 warnings generated. [ 29% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -MF apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o.d -o apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp FAILED: [code=1] apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -MF apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o.d -o apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::QualityExtractor' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:491:67: note: in instantiation of template class 'seqan::ModifiedString, seqan::ModView>>' requested here 491 | ModifiedString > quals(seq); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:433:5: note: in instantiation of function template specialization 'seqan::writeRecord>, seqan::StreamIterator>>, std::string, seqan::String>' requested here 433 | writeRecord(file.iter, meta, seq, Tag(), context(file).options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:471:9: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::TagFastq_>' requested here 471 | writeRecord(file, meta, seq, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:479:5: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::Tag>, std::string, seqan::String, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here 479 | writeRecord(file, meta, seq, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:976:9: note: in instantiation of function template specialization 'seqan::writeRecord>' requested here 976 | writeRecord(outMethLevelStream, idTop.str(), levels.forward); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'unary_function, char>' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::QualityExtractor>' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:491:67: note: in instantiation of template class 'seqan::ModifiedString>, seqan::ModView>>>' requested here 491 | ModifiedString > quals(seq); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:433:5: note: in instantiation of function template specialization 'seqan::writeRecord>, seqan::StreamIterator>>, seqan::String, seqan::String>>' requested here 433 | writeRecord(file.iter, meta, seq, Tag(), context(file).options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:471:9: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::String>, seqan::TagFastq_>' requested here 471 | writeRecord(file, meta, seq, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:479:5: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::Tag>, seqan::String, seqan::String>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here 479 | writeRecord(file, meta, seq, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:1124:9: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::String>>' requested here 1124 | writeRecord(outSeqStream, id, seqVariants); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, char>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp 1. parser at end of file 2. Code generation 3. Running pass 'Function Pass Manager' on module '/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp'. 4. Running pass 'Two-Address instruction pass' on function '@_ZN5seqan11writeHeaderINS_4IterINS_13VirtualStreamIcNS_3TagINS_7Output_EEENSt3__111char_traitsIcEEEENS_14StreamIteratorIS5_EEEENS_9StringSetINS_6StringIcNS_5AllocIvEEEENS_5OwnerINS3_INS_8Default_EEEEEEENS_14NameStoreCacheISM_SH_EENS_9DependentINS3_INS_10TagInsist_EEEEEEEvRT_RKNSE_INS_15VcfHeaderRecordESG_EERNS_12VcfIOContextIT0_T1_T2_EERKNS3_INS_4Vcf_EEE' #0 0x0000010312eb60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x0000010312eb3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x0000010312e643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00000103174302dc (/lib/libthr.so.3+0x1a2dc) #4 0x000001031742f8eb (/lib/libthr.so.3+0x198eb) #5 0x0000010309e7d2d3 ([vdso]+0x2d3) #6 0x0000010311fd851e std::__1::pair, llvm::detail::DenseMapPair, false>, bool> llvm::DenseMapBase, llvm::detail::DenseMapPair>, llvm::MachineInstr*, unsigned int, llvm::DenseMapInfo, llvm::detail::DenseMapPair>::try_emplace(llvm::MachineInstr*&&, unsigned int&&) (/usr/lib/libprivatellvm.so.19+0x29d851e) #7 0x000001031253672a (/usr/lib/libprivatellvm.so.19+0x2f3672a) #8 0x000001031253913b (/usr/lib/libprivatellvm.so.19+0x2f3913b) #9 0x000001031209427d llvm::MachineFunctionPass::runOnFunction(llvm::Function&) (/usr/lib/libprivatellvm.so.19+0x2a9427d) #10 0x00000103128a34c2 llvm::FPPassManager::runOnFunction(llvm::Function&) (/usr/lib/libprivatellvm.so.19+0x32a34c2) #11 0x00000103128a9104 llvm::FPPassManager::runOnModule(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a9104) #12 0x00000103128a3d13 llvm::legacy::PassManagerImpl::run(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a3d13) #13 0x000001030d46cce3 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr, std::__1::unique_ptr>, clang::BackendConsumer*) (/usr/lib/libprivateclang.so.19+0x226cce3) #14 0x000001030d80aef3 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/usr/lib/libprivateclang.so.19+0x260aef3) #15 0x000001030de8fd29 clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fd29) #16 0x000001030dd21189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #17 0x000001030dc9e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #18 0x000001030dda779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #19 0x000000fae9b5089e (/usr/bin/c+++0xd89e) #20 0x000000fae9b5dd53 (/usr/bin/c+++0x1ad53) #21 0x000001030d97d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #22 0x0000010312e64146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #23 0x000001030d97cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #24 0x000001030d940af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #25 0x000001030d940d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #26 0x000001030d95d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #27 0x000000fae9b5d4c8 (/usr/bin/c+++0x1a4c8) #28 0x000000fae9b5ba92 (/usr/bin/c+++0x18a92) #29 0x000001031a28037f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 138 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/mason_variator-660af6.cpp c++: note: diagnostic msg: /tmp/mason_variator-660af6.sh c++: note: diagnostic msg: ******************** [ 30% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o -MF apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o.d -o apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp FAILED: [code=1] apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o -MF apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o.d -o apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:46: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar_score.h:28:57: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 28 | struct FunctorDna5OrdValueComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:122:14: warning: variable 'matches' set but not used [-Wunused-but-set-variable] 122 | unsigned matches = 0; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:1049:9: warning: variable 'helper' set but not used [-Wunused-but-set-variable] 1049 | int helper = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:21:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 21 | if (!open(seqFileIn, toCString(fileName))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:9: note: in instantiation of function template specialization 'loadReadsCroppedId, seqan::String>' requested here 996 | loadReadsCroppedId(store, options.readFileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:9: note: in instantiation of function template specialization 'postProcessMain>' requested here 294 | postProcessMain(options, BsNonSimple()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:596:12: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 596 | return open(stream, fileStream, stream.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:231:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here 231 | readRecord(meta, seq, file, static_cast::Base const & >(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:296:5: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>>' requested here 296 | readRecord(meta, seq, file, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:29:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>>' requested here 29 | readRecord(_id, seq, seqFileIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:9: note: in instantiation of function template specialization 'loadReadsCroppedId, seqan::String>' requested here 996 | loadReadsCroppedId(store, options.readFileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:9: note: in instantiation of function template specialization 'postProcessMain>' requested here 294 | postProcessMain(options, BsNonSimple()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment, seqan::PrefixSegment>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:464:12: note: in implicit copy constructor for 'seqan::Segment, seqan::PrefixSegment>' first required here 464 | return typename Prefix::Type(t, pos_end); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:1055:86: note: in instantiation of function template specialization 'seqan::prefix, unsigned long>' requested here 1055 | if ((record.qName[length(record.qName)-2] == '/' && (!empty(currReadName) && prefix(record.qName, length(record.qName)-2) != prefix(currReadName, length(currReadName)-2) )) || | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:9: note: in instantiation of function template specialization 'postProcessMain>' requested here 294 | postProcessMain(options, BsNonSimple()); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:88: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: 'binary_function, seqan::GapAnchor, bool>' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:359:9: note: in instantiation of template class 'seqan::_LessGapAnchor, const seqan::Tag>' requested here 359 | _LessGapAnchor::Type, SortGapPos const>() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:662:28: note: in instantiation of function template specialization 'seqan::upperBoundGapAnchor>, int>' requested here 662 | me.anchorIdx = upperBoundGapAnchor(anchors, pos, SortGapPos()) - begin(anchors, Standard()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:93:9: note: in instantiation of function template specialization 'seqan::_goToGapAnchorIterator>, seqan::AnchorGaps>>>, seqan::GapsIterator>>>>, int>' requested here 93 | _goToGapAnchorIterator(*this, data_container->data_viewCutBegin + data_container->data_cutBegin); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:523:12: note: in instantiation of member function 'seqan::Iter>, seqan::AnchorGaps>>>, seqan::GapsIterator>>>>::Iter' requested here 523 | return typename Iterator > >::Type(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:362:12: note: in instantiation of function template specialization 'seqan::begin>, seqan::String>>' requested here 362 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:368:43: note: in instantiation of function template specialization 'seqan::begin>, seqan::AnchorGaps>>>>' requested here 368 | typename Iterator::Type it1 = begin(gaps1); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:351:12: note: in instantiation of function template specialization 'seqan::getCigarString, seqan::Gaps>, seqan::AnchorGaps>>>, seqan::Gaps>, seqan::AnchorGaps>>>, int>' requested here 351 | return getCigarString(cigar, gaps1, gaps2, 20); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:242:5: note: in instantiation of function template specialization 'seqan::getCigarString>, seqan::Gaps>, seqan::AnchorGaps>>>, seqan::Gaps>, seqan::AnchorGaps>>>>' requested here 242 | getCigarString(cigar, contigGaps, readGaps); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:1073:25: note: in instantiation of function template specialization 'writeBsAlignment, seqan::Gaps>, seqan::AnchorGaps>>>, unsigned int, double, AppOptions>' requested here 1073 | writeBsAlignment(bamFileOut, store, setContigGaps[verifiedMates.alignedReadIdL], verifiedMates.alignedReadIdL, verifiedMates.mapqL, verifiedMates.recordL, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:9: note: in instantiation of function template specialization 'postProcessMain>' requested here 294 | postProcessMain(options, BsNonSimple()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::GapAnchor, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:88: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: 'binary_function, seqan::GapAnchor, bool>' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:327:9: note: in instantiation of template class 'seqan::_LessGapAnchor, const seqan::Tag>' requested here 327 | _LessGapAnchor::Type, SortSeqPos const>() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:848:25: note: in instantiation of function template specialization 'seqan::upperBoundGapAnchor>, unsigned long>' requested here 848 | anchorIdx = upperBoundGapAnchor(anchors, pos, SortSeqPos()) - begin(anchors, Standard()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:874:12: note: in instantiation of function template specialization 'seqan::positionSeqToGap>, seqan::String>, unsigned long>' requested here 874 | return positionSeqToGap(gaps, sourcePosition) - gaps.data_viewCutBegin - gaps.data_cutBegin; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:611:35: note: in instantiation of function template specialization 'seqan::toViewPosition>, seqan::String>, unsigned long>' requested here 611 | setClippedBeginPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:105:5: note: in instantiation of function template specialization 'seqan::setBeginPosition>, seqan::String>, unsigned long>' requested here 105 | setBeginPosition(readGaps, beginPosition(readGaps)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:1168:9: note: in instantiation of function template specialization 'reAlign4>, seqan::AnchorGaps>>>, seqan::Gaps>, seqan::AnchorGaps>>>, seqan::FragmentStore, unsigned int, seqan::Score, seqan::Tag, seqan::Tag>>, seqan::Score, seqan::Tag, seqan::Tag>>, seqan::Score, seqan::Tag, seqan::Tag>>, seqan::Score, seqan::Tag, seqan::Tag>>, AppOptions>' requested here 1168 | reAlign4(readGaps, contigGaps, store, id, scoringSchemeCTLeft, scoringSchemeCTRight, scoringSchemeGALeft, scoringSchemeGARight, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:9: note: in instantiation of function template specialization 'postProcessMain>' requested here 294 | postProcessMain(options, BsNonSimple()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::GapAnchor, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp 1. parser at end of file 2. Optimizer 3. Running pass "require,function(invalidate),require,cgscc(devirt<4>(inline,function-attrs,openmp-opt-cgscc,function(sroa,early-cse,speculative-execution,jump-threading,correlated-propagation,simplifycfg,instcombine,aggressive-instcombine,libcalls-shrinkwrap,tailcallelim,simplifycfg,reassociate,constraint-elimination,loop-mssa(loop-instsimplify,loop-simplifycfg,licm,loop-rotate,licm,simple-loop-unswitch),simplifycfg,instcombine,loop(loop-idiom,indvars,simple-loop-unswitch,loop-deletion,loop-unroll-full),sroa,vector-combine,mldst-motion,gvn<>,sccp,bdce,instcombine,jump-threading,correlated-propagation,adce,memcpyopt,dse,move-auto-init,loop-mssa(licm),coro-elide,simplifycfg,instcombine),function-attrs,function(require),coro-split)),function(invalidate),cgscc(devirt<4>())" on module "/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp" 4. Running pass "cgscc(devirt<4>(inline,function-attrs,openmp-opt-cgscc,function(sroa,early-cse,speculative-execution,jump-threading,correlated-propagation,simplifycfg,instcombine,aggressive-instcombine,libcalls-shrinkwrap,tailcallelim,simplifycfg,reassociate,constraint-elimination,loop-mssa(loop-instsimplify,loop-simplifycfg,licm,loop-rotate,licm,simple-loop-unswitch),simplifycfg,instcombine,loop(loop-idiom,indvars,simple-loop-unswitch,loop-deletion,loop-unroll-full),sroa,vector-combine,mldst-motion,gvn<>,sccp,bdce,instcombine,jump-threading,correlated-propagation,adce,memcpyopt,dse,move-auto-init,loop-mssa(licm),coro-elide,simplifycfg,instcombine),function-attrs,function(require),coro-split))" on module "/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp" 5. Running pass "correlated-propagation" on function "_ZN5seqaneqIKNS_6StringIcNS_5AllocIvEEEENS_12InfixSegmentEA3_cEEbRKNS_7SegmentIT_T0_EERKT1_" #0 0x00002294268b60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x00002294268b3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x00002294268643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x0000229421f642dc (/lib/libthr.so.3+0x1a2dc) #4 0x0000229421f638eb (/lib/libthr.so.3+0x198eb) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/bisar-96ef48.cpp c++: note: diagnostic msg: /tmp/bisar-96ef48.sh c++: note: diagnostic msg: ******************** [ 31% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/bam2roi.dir/bam2roi.cpp.o -MF apps/ngs_roi/CMakeFiles/bam2roi.dir/bam2roi.cpp.o.d -o apps/ngs_roi/CMakeFiles/bam2roi.dir/bam2roi.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 20 warnings generated. [ 31% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp FAILED: [code=1] apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp 1. parser at end of file 2. Code generation 3. Running pass 'Function Pass Manager' on module '/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp'. 4. Releasing pass 'Live Interval Analysis' #0 0x000035884feb60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x000035884feb3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x000035884fe643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00003588532322dc (/lib/libthr.so.3+0x1a2dc) #4 0x00003588532318eb (/lib/libthr.so.3+0x198eb) #5 0x0000358845b772d3 ([vdso]+0x2d3) #6 0x000035885563b8fd (/lib/libc.so.7+0x18c8fd) #7 0x000035885563296d (/lib/libc.so.7+0x18396d) #8 0x000035884efbe6ad llvm::LiveIntervals::clear() (/usr/lib/libprivatellvm.so.19+0x29be6ad) #9 0x000035884f8a6fd5 llvm::PMDataManager::freePass(llvm::Pass*, llvm::StringRef, llvm::PassDebuggingString) (/usr/lib/libprivatellvm.so.19+0x32a6fd5) #10 0x000035884f8a6eec llvm::PMDataManager::removeDeadPasses(llvm::Pass*, llvm::StringRef, llvm::PassDebuggingString) (/usr/lib/libprivatellvm.so.19+0x32a6eec) #11 0x000035884f8a35f7 llvm::FPPassManager::runOnFunction(llvm::Function&) (/usr/lib/libprivatellvm.so.19+0x32a35f7) #12 0x000035884f8a9104 llvm::FPPassManager::runOnModule(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a9104) #13 0x000035884f8a3d13 llvm::legacy::PassManagerImpl::run(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a3d13) #14 0x0000358849c6cce3 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr, std::__1::unique_ptr>, clang::BackendConsumer*) (/usr/lib/libprivateclang.so.19+0x226cce3) #15 0x000035884a00aef3 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/usr/lib/libprivateclang.so.19+0x260aef3) #16 0x000035884a68fd29 clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fd29) #17 0x000035884a521189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #18 0x000035884a49e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #19 0x000035884a5a779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #20 0x0000358024a9189e (/usr/bin/c+++0xd89e) #21 0x0000358024a9ed53 (/usr/bin/c+++0x1ad53) #22 0x000035884a17d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #23 0x000035884fe64146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #24 0x000035884a17cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #25 0x000035884a140af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #26 0x000035884a140d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #27 0x000035884a15d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #28 0x0000358024a9e4c8 (/usr/bin/c+++0x1a4c8) #29 0x0000358024a9ca92 (/usr/bin/c+++0x18a92) #30 0x000035885554037f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/pair_align_global-374b88.cpp c++: note: diagnostic msg: /tmp/pair_align_global-374b88.sh c++: note: diagnostic msg: ******************** [ 32% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -MF apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o.d -o apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagGff_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:152:18: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 152 | if (!open(gffFileIn, toCString(options.inputGffFile))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagGtf_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:152:18: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 152 | if (!open(gffFileIn, toCString(options.inputGffFile))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'unary_function, char>' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::QualityExtractor>' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:491:67: note: in instantiation of template class 'seqan::ModifiedString>, seqan::ModView>>>' requested here 491 | ModifiedString > quals(seq); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:433:5: note: in instantiation of function template specialization 'seqan::writeRecord>, seqan::StreamIterator>>, std::string, seqan::String>>' requested here 433 | writeRecord(file.iter, meta, seq, Tag(), context(file).options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:471:9: note: in instantiation of function template specialization 'seqan::writeRecord>, seqan::TagFastq_>' requested here 471 | writeRecord(file, meta, seq, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:479:5: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::Tag>, std::string, seqan::String>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here 479 | writeRecord(file, meta, seq, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:331:17: note: in instantiation of function template specialization 'seqan::writeRecord>>' requested here 331 | writeRecord(seqFileOut, ss.str(), transcript); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, char>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 23 warnings generated. [ 33% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig<>>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig<>>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig<>>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig<>>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig<>>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig<>>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig<>, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig<>>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig<>>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig<>>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig<>, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig<>>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig<>>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig<>>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig<>, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig<>>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig<>>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig<>>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ 18 warnings generated. [ 34% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ 18 warnings generated. [ 34% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ 18 warnings generated. [ 35% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fiona/CMakeFiles/compute_gain.dir/compute_gain.cpp.o -MF apps/fiona/CMakeFiles/compute_gain.dir/compute_gain.cpp.o.d -o apps/fiona/CMakeFiles/compute_gain.dir/compute_gain.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:13: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:542:35: warning: variable 'errors' set but not used [-Wunused-but-set-variable] 542 | unsigned readPos = 0, errors = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:907:19: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 907 | success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:596:12: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 596 | return open(stream, fileStream, stream.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:231:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here 231 | readRecord(meta, seq, file, static_cast::Base const & >(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:296:5: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>>' requested here 296 | readRecord(meta, seq, file, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:342:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>>' requested here 342 | readRecord(context(file).buffer[0], seqBuffer, file); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:362:5: note: in instantiation of function template specialization 'seqan::readRecords>, seqan::StringSet>>, void, unsigned long>' requested here 362 | readRecords(meta, seq, file, std::numeric_limits::max()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:950:9: note: in instantiation of function template specialization 'seqan::readRecords>, seqan::StringSet>>, void>' requested here 950 | readRecords(ids, seqs, inGenome); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:97: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: warning: definition of implicit copy constructor for 'Align>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 104 | Align & operator=(Align const & other) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:98:8: note: in implicit copy constructor for 'seqan::Align>>' first required here 98 | struct Stats | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:36: note: in implicit move constructor for 'Stats' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:19: note: in instantiation of function template specialization 'seqan::ValueConstructor_::construct' requested here 305 | TConstructor::construct(it, std::forward(param_)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:9: note: in instantiation of function template specialization 'seqan::valueConstruct' requested here 511 | valueConstruct(target_begin, std::move(*source_begin)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:5: note: in instantiation of function template specialization 'seqan::_arrayConstructMoveDefault' requested here 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:5: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:5: note: in instantiation of function template specialization 'seqan::_reserveStorage, unsigned long, seqan::TagGenerous_>' requested here 1697 | _reserveStorage(seq, new_capacity, tag); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:38: note: in instantiation of function template specialization 'seqan::reserve, unsigned long, seqan::TagGenerous_>' requested here 1725 | TSize new_capacity = reserve(me, new_length, TExpand()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:43: note: in instantiation of function template specialization 'seqan::_Resize_String>::resize_>' requested here 1785 | return _Resize_String >::resize_(me, new_length); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:12: note: in instantiation of function template specialization 'seqan::resize, int, seqan::TagGenerous_>' requested here 1149 | return resize(std::forward(me), new_length, typename DefaultOverflowExplicit::Type()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:986:5: note: in instantiation of function template specialization 'seqan::resize &, int>' requested here 986 | resize(stats, options.numThreads); | ^ 22 warnings generated. [ 36% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp FAILED: [code=1] apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp 1. parser at end of file 2. Code generation 3. Running pass 'Function Pass Manager' on module '/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp'. 4. Releasing pass 'Live Interval Analysis' #0 0x00002d2b550b60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x00002d2b550b3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x00002d2b550643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00002d2b5a1f42dc (/lib/libthr.so.3+0x1a2dc) #4 0x00002d2b5a1f38eb (/lib/libthr.so.3+0x198eb) #5 0x00002d2b4c0ef2d3 ([vdso]+0x2d3) #6 0x00002d2b541b5048 llvm::LiveInterval::clearSubRanges() (/usr/lib/libprivatellvm.so.19+0x29b5048) #7 0x00002d2b541be595 llvm::LiveIntervals::clear() (/usr/lib/libprivatellvm.so.19+0x29be595) #8 0x00002d2b54aa6fd5 llvm::PMDataManager::freePass(llvm::Pass*, llvm::StringRef, llvm::PassDebuggingString) (/usr/lib/libprivatellvm.so.19+0x32a6fd5) #9 0x00002d2b54aa6eec llvm::PMDataManager::removeDeadPasses(llvm::Pass*, llvm::StringRef, llvm::PassDebuggingString) (/usr/lib/libprivatellvm.so.19+0x32a6eec) #10 0x00002d2b54aa35f7 llvm::FPPassManager::runOnFunction(llvm::Function&) (/usr/lib/libprivatellvm.so.19+0x32a35f7) #11 0x00002d2b54aa9104 llvm::FPPassManager::runOnModule(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a9104) #12 0x00002d2b54aa3d13 llvm::legacy::PassManagerImpl::run(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a3d13) #13 0x00002d2b4f26cce3 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr, std::__1::unique_ptr>, clang::BackendConsumer*) (/usr/lib/libprivateclang.so.19+0x226cce3) #14 0x00002d2b4f60aef3 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/usr/lib/libprivateclang.so.19+0x260aef3) #15 0x00002d2b4fc8fd29 clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fd29) #16 0x00002d2b4fb21189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #17 0x00002d2b4fa9e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #18 0x00002d2b4fba779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #19 0x00002d232af8689e (/usr/bin/c+++0xd89e) #20 0x00002d232af93d53 (/usr/bin/c+++0x1ad53) #21 0x00002d2b4f77d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #22 0x00002d2b55064146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #23 0x00002d2b4f77cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #24 0x00002d2b4f740af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #25 0x00002d2b4f740d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #26 0x00002d2b4f75d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #27 0x00002d232af934c8 (/usr/bin/c+++0x1a4c8) #28 0x00002d232af91a92 (/usr/bin/c+++0x18a92) #29 0x00002d2b5bbb237f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/pair_align_global-b7ac1c.cpp c++: note: diagnostic msg: /tmp/pair_align_global-b7ac1c.sh c++: note: diagnostic msg: ******************** [ 36% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ 18 warnings generated. [ 37% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ 18 warnings generated. [ 38% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp FAILED: [code=1] apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp 1. parser at end of file 2. Code generation 3. Running pass 'Function Pass Manager' on module '/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp'. 4. Running pass 'Loop Pass Manager' on function '@_ZN5seqan9StringSetINS_6StringIcNS_5AllocIvEEEENS_9DependentINS_3TagINS_10TagInsist_EEEEEEC2INS6_INS_8Default_EEEEERKNS0_IS4_NS_5OwnerIT_EEEE' 5. Running pass 'Loop Strength Reduction' on basic block '%25' #0 0x00002160c9eb60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x00002160c9eb3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x00002160c9e643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00002160cc3d62dc (/lib/libthr.so.3+0x1a2dc) #4 0x00002160cc3d58eb (/lib/libthr.so.3+0x198eb) #5 0x00002160be4f92d3 ([vdso]+0x2d3) #6 0x00002160c8a79ec7 std::__1::pair, llvm::detail::DenseSetPair, false>, bool> llvm::DenseMapBase, llvm::detail::DenseSetPair>, llvm::Type*, llvm::detail::DenseSetEmpty, llvm::DenseMapInfo, llvm::detail::DenseSetPair>::try_emplace(llvm::Type* const&, llvm::detail::DenseSetEmpty&) (/usr/lib/libprivatellvm.so.19+0x2479ec7) #7 0x00002160cae9a48f llvm::SetVector, llvm::DenseSet>, 4u>::insert(llvm::Type* const&) (/usr/lib/libprivatellvm.so.19+0x489a48f) #8 0x00002160cae88897 (/usr/lib/libprivatellvm.so.19+0x4888897) #9 0x00002160cae84d47 (/usr/lib/libprivatellvm.so.19+0x4884d47) #10 0x00002160caea7b35 (/usr/lib/libprivatellvm.so.19+0x48a7b35) #11 0x00002160c8a9a7ee llvm::LPPassManager::runOnFunction(llvm::Function&) (/usr/lib/libprivatellvm.so.19+0x249a7ee) #12 0x00002160c98a34c2 llvm::FPPassManager::runOnFunction(llvm::Function&) (/usr/lib/libprivatellvm.so.19+0x32a34c2) #13 0x00002160c98a9104 llvm::FPPassManager::runOnModule(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a9104) #14 0x00002160c98a3d13 llvm::legacy::PassManagerImpl::run(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a3d13) #15 0x00002160c2a6cce3 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr, std::__1::unique_ptr>, clang::BackendConsumer*) (/usr/lib/libprivateclang.so.19+0x226cce3) #16 0x00002160c2e0aef3 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/usr/lib/libprivateclang.so.19+0x260aef3) #17 0x00002160c348fd29 clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fd29) #18 0x00002160c3321189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #19 0x00002160c329e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #20 0x00002160c33a779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #21 0x000021589c8c689e (/usr/bin/c+++0xd89e) #22 0x000021589c8d3d53 (/usr/bin/c+++0x1ad53) #23 0x00002160c2f7d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #24 0x00002160c9e64146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #25 0x00002160c2f7cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #26 0x00002160c2f40af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #27 0x00002160c2f40d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #28 0x00002160c2f5d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #29 0x000021589c8d34c8 (/usr/bin/c+++0x1a4c8) #30 0x000021589c8d1a92 (/usr/bin/c+++0x18a92) #31 0x00002160ceeff37f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/pair_align_global-a12b11.cpp c++: note: diagnostic msg: /tmp/pair_align_global-a12b11.sh c++: note: diagnostic msg: ******************** [ 39% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ 18 warnings generated. [ 39% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -MF apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o.d -o apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:55: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:51: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 20 warnings generated. [ 40% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ 18 warnings generated. [ 41% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ 18 warnings generated. [ 41% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o -MF apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o.d -o apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:24: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:13: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:838:15: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 838 | BamFileIn inSam(toCString(options.nameSAM)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:838:15: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 838 | BamFileIn inSam(toCString(options.nameSAM)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:838:15: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 838 | BamFileIn inSam(toCString(options.nameSAM)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:838:15: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 838 | BamFileIn inSam(toCString(options.nameSAM)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:13: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:838:15: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 838 | BamFileIn inSam(toCString(options.nameSAM)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:17: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:88: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: 'binary_function, seqan::GapAnchor, bool>' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:359:9: note: in instantiation of template class 'seqan::_LessGapAnchor, const seqan::Tag>' requested here 359 | _LessGapAnchor::Type, SortGapPos const>() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:662:28: note: in instantiation of function template specialization 'seqan::upperBoundGapAnchor>, int>' requested here 662 | me.anchorIdx = upperBoundGapAnchor(anchors, pos, SortGapPos()) - begin(anchors, Standard()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:93:9: note: in instantiation of function template specialization 'seqan::_goToGapAnchorIterator>>, seqan::AnchorGaps>>>, seqan::GapsIterator>>>>, int>' requested here 93 | _goToGapAnchorIterator(*this, data_container->data_viewCutBegin + data_container->data_cutBegin); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:523:12: note: in instantiation of member function 'seqan::Iter>>, seqan::AnchorGaps>>>, seqan::GapsIterator>>>>::Iter' requested here 523 | return typename Iterator > >::Type(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:362:12: note: in instantiation of function template specialization 'seqan::begin>>, seqan::String>>' requested here 362 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:639:41: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 639 | typename Iterator::Type it = begin(gaps); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:331:5: note: in instantiation of function template specialization 'seqan::_readAlignments, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::StringSet>, seqan::NameStoreCache>>, seqan::Dependent<>, seqan::Iter>, seqan::StreamIterator>>, seqan::Tag>' requested here 331 | _readAlignments(store, contigAnchorGaps, matchMateInfos, ctx, iter, format, importFlags); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:5: note: in instantiation of function template specialization 'seqan::readRecords, seqan::StringSet>, seqan::NameStoreCache>>, seqan::Dependent<>, seqan::Iter>, seqan::StreamIterator>>, seqan::Tag>' requested here 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:5: note: in instantiation of function template specialization 'seqan::readRecords, seqan::Tag, void>' requested here 373 | readRecords(store, bamFile, FragStoreImportFlags()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:839:5: note: in instantiation of function template specialization 'seqan::readRecords, seqan::Tag, void>' requested here 839 | readRecords(fragStore, inSam); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::GapAnchor, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:17: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:62: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: 'binary_function>, seqan::AlignedReadStoreElement>, bool>' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2363:58: note: in instantiation of template class 'seqan::LessConvertPairWiseToGlobalAlignment>' requested here 2363 | LessConvertPairWiseToGlobalAlignment lessFunctor(store, offsetRecord); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:9: note: in instantiation of function template specialization 'seqan::convertPairWiseToGlobalAlignment, seqan::StringSet>, seqan::Owner>>>' requested here 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:5: note: in instantiation of function template specialization 'seqan::readRecords, seqan::StringSet>, seqan::NameStoreCache>>, seqan::Dependent<>, seqan::Iter>, seqan::StreamIterator>>, seqan::Tag>' requested here 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:5: note: in instantiation of function template specialization 'seqan::readRecords, seqan::Tag, void>' requested here 373 | readRecords(store, bamFile, FragStoreImportFlags()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:839:5: note: in instantiation of function template specialization 'seqan::readRecords, seqan::Tag, void>' requested here 839 | readRecords(fragStore, inSam); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::AlignedReadStoreElement>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:17: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:88: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: 'binary_function, seqan::GapAnchor, bool>' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:327:9: note: in instantiation of template class 'seqan::_LessGapAnchor, const seqan::Tag>' requested here 327 | _LessGapAnchor::Type, SortSeqPos const>() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:848:25: note: in instantiation of function template specialization 'seqan::upperBoundGapAnchor>, long>' requested here 848 | anchorIdx = upperBoundGapAnchor(anchors, pos, SortSeqPos()) - begin(anchors, Standard()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2408:18: note: in instantiation of function template specialization 'seqan::positionSeqToGap, seqan::String>, long>' requested here 2408 | cBegin = positionSeqToGap(contigGapsGlobal, cBegin); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:9: note: in instantiation of function template specialization 'seqan::convertPairWiseToGlobalAlignment, seqan::StringSet>, seqan::Owner>>>' requested here 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:5: note: in instantiation of function template specialization 'seqan::readRecords, seqan::StringSet>, seqan::NameStoreCache>>, seqan::Dependent<>, seqan::Iter>, seqan::StreamIterator>>, seqan::Tag>' requested here 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:5: note: in instantiation of function template specialization 'seqan::readRecords, seqan::Tag, void>' requested here 373 | readRecords(store, bamFile, FragStoreImportFlags()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:839:5: note: in instantiation of function template specialization 'seqan::readRecords, seqan::Tag, void>' requested here 839 | readRecords(fragStore, inSam); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::GapAnchor, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagGff_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:848:15: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 848 | GffFileIn inGff(toCString(options.nameGFF)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagGtf_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:9: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::True>' requested here 257 | _open(*this, fileName, openMode, True()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:848:15: note: in instantiation of member function 'seqan::FormattedFile, seqan::Tag>::FormattedFile' requested here 848 | GffFileIn inGff(toCString(options.nameGFF)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:13: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment, seqan::PrefixSegment>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:471:12: note: in implicit copy constructor for 'seqan::Segment, seqan::PrefixSegment>' first required here 471 | return typename Prefix::Type(t, pos_end); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:660:17: note: in instantiation of function template specialization 'seqan::prefix, int>' requested here 660 | if (prefix(name, 2) == "__" && infix(name, 2, 2 + length(type)) == type && name[2 + length(type)] == '_') | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io_gff.h:351:5: note: in instantiation of function template specialization 'seqan::_storeRemoveTempAnnoNames, void>' requested here 351 | _storeRemoveTempAnnoNames(fragStore); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:849:5: note: in instantiation of function template specialization 'seqan::readRecords>' requested here 849 | readRecords(fragStore, inGff); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:17: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:61: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: warning: definition of implicit copy constructor for 'Iter, seqan::AnnotationTree<>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 272 | operator = (Iter const &_origin) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:41:16: note: in implicit copy constructor for 'seqan::Iter, seqan::AnnotationTree<>>' first required here 41 | TIter it = begin(fragStore, AnnotationTree<>()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:851:2: note: in instantiation of function template specialization 'seqan::adjustParentEntries>' requested here 851 | adjustParentEntries(fragStore); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:12: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:86: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: warning: definition of implicit copy assignment operator for 'Iter>, seqan::CountingIteratorImpl_>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 105 | Iter(Iter const & other_) : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:90:6: note: in implicit copy assignment operator for 'seqan::Iter>, seqan::CountingIteratorImpl_>>' first required here 90 | itR = begin(ids); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/fusion.h:754:5: note: in instantiation of function template specialization 'seqan::getIdsForRead>, void, seqan::FragmentStoreConfig<>, seqan::IntervalTree, seqan::String>>' requested here 754 | getIdsForRead(ids, fragStore, *intervalTree, getValue(it).intervals, offsetInterval); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:3: note: in instantiation of function template specialization 'seqan::getResults_Fusion>, seqan::String, seqan::String>, seqan::String>, void, seqan::FragmentStoreConfig<>>' requested here 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:12: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:86: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:71: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/iterator_counting.h:74:5: warning: definition of implicit copy assignment operator for 'Iter>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 74 | Iter(Iter const & other) : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:81:7: note: in implicit copy assignment operator for 'seqan::Iter>' first required here 81 | class Iter : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:90:6: note: in implicit copy assignment operator for 'seqan::Iter>, seqan::CountingIteratorImpl_>>' first required here 90 | itR = begin(ids); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/fusion.h:754:5: note: in instantiation of function template specialization 'seqan::getIdsForRead>, void, seqan::FragmentStoreConfig<>, seqan::IntervalTree, seqan::String>>' requested here 754 | getIdsForRead(ids, fragStore, *intervalTree, getValue(it).intervals, offsetInterval); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:3: note: in instantiation of function template specialization 'seqan::getResults_Fusion>, seqan::String, seqan::String>, seqan::String>, void, seqan::FragmentStoreConfig<>>' requested here 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:16: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: warning: definition of implicit copy assignment operator for 'IntervalTreeNode>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1441:18: note: in implicit copy assignment operator for 'seqan::IntervalTreeNode>' first required here 1441 | act_prop = property(pm, act_knot); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_intervaltree.h:182:5: note: in instantiation of function template specialization 'seqan::findIntervals>, seqan::String>>, unsigned int, unsigned int>' requested here 182 | findIntervals(result1, intervalTree.g, intervalTree.pm, interval.i1 + offsetInterval); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:85:3: note: in instantiation of function template specialization 'seqan::findIntervalsForInterval, seqan::Interval, unsigned int>' requested here 85 | findIntervalsForInterval(value(itR), intervalTree, getValue(itI), offsetInterval); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/fusion.h:754:5: note: in instantiation of function template specialization 'seqan::getIdsForRead>, void, seqan::FragmentStoreConfig<>, seqan::IntervalTree, seqan::String>>' requested here 754 | getIdsForRead(ids, fragStore, *intervalTree, getValue(it).intervals, offsetInterval); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:3: note: in instantiation of function template specialization 'seqan::getResults_Fusion>, seqan::String, seqan::String>, seqan::String>, void, seqan::FragmentStoreConfig<>>' requested here 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:5: note: in instantiation of function template specialization 'seqan::ngsOverlapper' requested here 199 | ngsOverlapper(options); | ^ 27 warnings generated. [ 42% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ 18 warnings generated. [ 43% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -MF apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o.d -o apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:179:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 179 | if (!open(fin, toCString(filename))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:288:9: note: in instantiation of function template specialization 'seqan::loadScoreMatrix, seqan::Tag>' requested here 288 | loadScoreMatrix(sc, toCString(options.matrix)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:57: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 86 | if (!open(inFile, fileName)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:5: note: in instantiation of function template specialization '_loadSequences>>, seqan::StringSet>>' requested here 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:5: note: in instantiation of function template specialization 'pairwise_align, seqan::AlignConfig, seqan::Score>, std::string, seqan::Tag, int, std::string>' requested here 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:9: note: in instantiation of function template specialization '_initAlignParams, seqan::Score>, seqan::Tag, seqan::AlignConfig>' requested here 289 | _initAlignParams(options, sc, alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:36: note: in instantiation of function template specialization '_initScoreMatrix, seqan::AlignConfig>' requested here 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: note: in instantiation of function template specialization 'pairAlignConfig, seqan::AlignConfig>' requested here 73 | PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:68:9: note: expanded from macro 'PAIR_ALIGN_DEFINE_GLOBAL_FUNC' 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ^ 18 warnings generated. [ 43% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"1.0.11\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/micro_razers/CMakeFiles/micro_razers.dir/micro_razers.cpp.o -MF apps/micro_razers/CMakeFiles/micro_razers.dir/micro_razers.cpp.o.d -o apps/micro_razers/CMakeFiles/micro_razers.dir/micro_razers.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:672:42: warning: 'binary_function, seqan::ReadMatch, bool>' is deprecated [-Wdeprecated-declarations] 672 | struct LessRNoEdistHLen : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1022:4: note: in instantiation of template class 'seqan::LessRNoEdistHLen>' requested here 1022 | LessRNoEdistHLen()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::ReadMatch, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:39: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:33: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/readSimulator.h:233:7: warning: variable 'lastOp' set but not used [-Wunused-but-set-variable] 233 | int lastOp = 0; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/readSimulator.h:178:6: warning: variable 'fragmentSize' set but not used [-Wunused-but-set-variable] 178 | int fragmentSize = readLength; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:379:18: warning: variable 'zeros' set but not used [-Wunused-but-set-variable] 379 | unsigned zeros = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:19: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 414 | success = open(options.readFile, toCString(readFileNames[0])); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:19: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 414 | success = open(options.readFile, toCString(readFileNames[0])); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:19: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 414 | success = open(options.readFile, toCString(readFileNames[0])); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:19: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 414 | success = open(options.readFile, toCString(readFileNames[0])); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:19: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 414 | success = open(options.readFile, toCString(readFileNames[0])); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:19: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 414 | success = open(options.readFile, toCString(readFileNames[0])); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:596:12: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::istream, seqan::TagSelector>>>' requested here 596 | return open(stream, fileStream, stream.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:651:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::istream, seqan::TagSelector>>>' requested here 651 | if (!open(file.stream, stream, compressionFormat)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:673:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, std::istream, seqan::TagSelector>>, seqan::False>' requested here 673 | return _open(file, stream, _mapFileFormatToCompressionFormat(file.format), False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:416:19: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void, std::istream>' requested here 416 | success = open(options.readFile, std::cin); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:91: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:268:5: warning: definition of implicit copy assignment operator for 'Index>, seqan::Owner>>, seqan::IndexQGram>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 268 | Index(Index &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>' first required here 110 | target = source; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>>' requested here 645 | assign(_dataValue(me), value_); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>>' requested here 594 | create(me, _dataValue(me)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram>>>' requested here 863 | create(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: in instantiation of function template specialization 'seqan::value>, seqan::Owner>>, seqan::IndexQGram>>>' requested here 339 | return value(me.data_host); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1666:27: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1666 | TReadSet &readSet = host(host(swiftPattern)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, seqan::String>, seqan::RazerSSpec<>>' requested here 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape<>, seqan::Tag>>' requested here 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2265:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape<>, seqan::Tag>>' requested here 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>>' requested here 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads>' requested here 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:188: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^ /usr/include/c++/v1/__type_traits/is_empty.h:22:71: note: in instantiation of template class 'seqan::RepeatLess_' requested here 22 | struct _LIBCPP_TEMPLATE_VIS is_empty : public integral_constant {}; | ^ /usr/include/c++/v1/map:627:18: note: in instantiation of template class 'std::is_empty>' requested here 627 | bool = is_empty<_Compare>::value && !__libcpp_is_final<_Compare>::value> | ^ /usr/include/c++/v1/map:994:11: note: in instantiation of default argument for '__map_value_compare' required here 994 | typedef __map_value_compare __vc; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:518:21: note: in instantiation of template class 'std::map, seqan::RepeatLess_>' requested here 518 | TRepeatList list; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:398:13: note: in instantiation of function template specialization 'seqan::findRepeats>, seqan::String>, int, int>' requested here 398 | findRepeats(data_repeats, haystack, minRepeatLen, maxPeriod); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1667:15: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1667 | TSwiftFinder swiftFinder(genome, options.repeatLength, 1); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, seqan::String>, seqan::RazerSSpec<>>' requested here 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape<>, seqan::Tag>>' requested here 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2265:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape<>, seqan::Tag>>' requested here 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>>' requested here 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads>' requested here 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:728:40: warning: 'binary_function, seqan::ReadMatch, bool>' is deprecated [-Wdeprecated-declarations] 728 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:859:3: note: in instantiation of template class 'seqan::LessRNoGEndPos>' requested here 859 | LessRNoGEndPos()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1742:21: note: in instantiation of function template specialization 'seqan::maskDuplicates>, seqan::RazerSOptions<>>' requested here 1742 | maskDuplicates(matches, options); // overlapping parallelograms cause duplicates | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, seqan::String>, seqan::RazerSSpec<>>' requested here 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape<>, seqan::Tag>>' requested here 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2265:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape<>, seqan::Tag>>' requested here 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>>' requested here 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads>' requested here 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::ReadMatch, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:643:37: warning: 'binary_function, seqan::ReadMatch, bool>' is deprecated [-Wdeprecated-declarations] 643 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:895:3: note: in instantiation of template class 'seqan::LessRNoGPos>' requested here 895 | LessRNoGPos()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1742:21: note: in instantiation of function template specialization 'seqan::maskDuplicates>, seqan::RazerSOptions<>>' requested here 1742 | maskDuplicates(matches, options); // overlapping parallelograms cause duplicates | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, seqan::String>, seqan::RazerSSpec<>>' requested here 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape<>, seqan::Tag>>' requested here 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2265:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape<>, seqan::Tag>>' requested here 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>>' requested here 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads>' requested here 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::ReadMatch, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:760:36: warning: 'binary_function, seqan::ReadMatch, bool>' is deprecated [-Wdeprecated-declarations] 760 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:925:3: note: in instantiation of template class 'seqan::LessErrors>' requested here 925 | LessErrors()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1742:21: note: in instantiation of function template specialization 'seqan::maskDuplicates>, seqan::RazerSOptions<>>' requested here 1742 | maskDuplicates(matches, options); // overlapping parallelograms cause duplicates | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, seqan::String>, seqan::RazerSSpec<>>' requested here 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape<>, seqan::Tag>>' requested here 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2265:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape<>, seqan::Tag>>' requested here 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>>' requested here 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads>' requested here 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::ReadMatch, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:91: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:268:5: warning: definition of implicit copy assignment operator for 'Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 268 | Index(Index &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>' first required here 110 | target = source; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 645 | assign(_dataValue(me), value_); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 594 | create(me, _dataValue(me)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 863 | create(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: in instantiation of function template specialization 'seqan::value>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 339 | return value(me.data_host); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1666:27: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1666 | TReadSet &readSet = host(host(swiftPattern)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, seqan::String>, seqan::RazerSSpec<>>' requested here 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape, seqan::OneGappedShape>, seqan::Tag>>' requested here 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2268:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape, seqan::OneGappedShape>, seqan::Tag>>' requested here 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>>' requested here 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads>' requested here 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:87: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: warning: definition of implicit copy assignment operator for 'Shape, seqan::OneGappedShape>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 107 | Shape(Shape const &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:52:57: note: in implicit copy assignment operator for 'seqan::Shape, seqan::OneGappedShape>' first required here 52 | template < typename TObject, typename TSpec > class Index; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>' first required here 110 | target = source; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 645 | assign(_dataValue(me), value_); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 594 | create(me, _dataValue(me)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>>' requested here 863 | create(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 339 | return value(me.data_host); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::OneGappedShape>>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, seqan::String>, seqan::RazerSSpec<>>' requested here 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape, seqan::OneGappedShape>, seqan::Tag>>' requested here 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2268:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape, seqan::OneGappedShape>, seqan::Tag>>' requested here 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>>' requested here 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads>' requested here 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:30: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:91: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:268:5: warning: definition of implicit copy assignment operator for 'Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 268 | Index(Index &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>' first required here 110 | target = source; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 645 | assign(_dataValue(me), value_); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 594 | create(me, _dataValue(me)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 863 | create(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: in instantiation of function template specialization 'seqan::value>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 339 | return value(me.data_host); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1666:27: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1666 | TReadSet &readSet = host(host(swiftPattern)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, seqan::String>, seqan::RazerSSpec<>>' requested here 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape, seqan::GappedShape>>, seqan::Tag>>' requested here 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2271:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape, seqan::GappedShape>>, seqan::Tag>>' requested here 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>>' requested here 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads>' requested here 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: warning: definition of implicit copy assignment operator for 'Shape, seqan::GappedShape>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 281 | Shape(Shape const &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:52:57: note: in implicit copy assignment operator for 'seqan::Shape, seqan::GappedShape>>' first required here 52 | template < typename TObject, typename TSpec > class Index; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>' first required here 110 | target = source; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 645 | assign(_dataValue(me), value_); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 594 | create(me, _dataValue(me)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>>' requested here 863 | create(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 339 | return value(me.data_host); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::String>, seqan::Index>, seqan::Owner>>, seqan::IndexQGram, seqan::GappedShape>>>>, seqan::Tag>, seqan::String>>, seqan::Myers>>, seqan::String>, seqan::RazerSSpec<>>' requested here 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape, seqan::GappedShape>>, seqan::Tag>>' requested here 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2271:11: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>, seqan::Shape, seqan::GappedShape>>, seqan::Tag>>' requested here 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads>, seqan::StringSet>, seqan::Owner>>, seqan::String>, seqan::RazerSSpec<>>' requested here 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads>' requested here 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:38: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/outputFormat.h:126:37: warning: 'binary_function, seqan::ReadMatch, bool>' is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/outputFormat.h:388:5: note: in instantiation of template class 'seqan::LessGPosRNo>' requested here 388 | LessGPosRNo()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:184:9: note: in instantiation of function template specialization 'seqan::dumpMatches>, seqan::StringSet>, seqan::StringSet>, seqan::Owner>>, seqan::StringSet>, seqan::String>, seqan::RazerSSpec<>>' requested here 184 | dumpMatches(matches, genomeNames, genomeFileNameList, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads>' requested here 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::ReadMatch, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 35 warnings generated. [ 44% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/bs_tools/CMakeFiles/casbar.dir/casbar.cpp.o -MF apps/bs_tools/CMakeFiles/casbar.dir/casbar.cpp.o.d -o apps/bs_tools/CMakeFiles/casbar.dir/casbar.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:60: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:73: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:6: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar_score.h:42:57: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 42 | struct FunctorDna5OrdValueComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:73: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:7: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar_consensus_realign.h:175:9: warning: variable 'help' set but not used [-Wunused-but-set-variable] 175 | int help = 0; // TODO rm | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1423:13: warning: variable 'numIndelsObservedF' set but not used [-Wunused-but-set-variable] 1423 | int numIndelsObservedF = 0; // if refGap then this counts the number of insertions on forward | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1424:13: warning: variable 'numIndelsObservedR' set but not used [-Wunused-but-set-variable] 1424 | int numIndelsObservedR = 0; // if refGap then this counts the number of insertions on reverse | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1426:13: warning: variable 'indelQualF' set but not used [-Wunused-but-set-variable] 1426 | int indelQualF = 0; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1427:13: warning: variable 'indelQualR' set but not used [-Wunused-but-set-variable] 1427 | int indelQualR = 0; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:94:18: warning: variable 'seqCount' set but not used [-Wunused-but-set-variable] 94 | unsigned seqCount = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:14: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 996 | if (!open(seqFile, toCString(fileNameList[f]))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:12: note: in instantiation of function template specialization 'seqan::loadContigs>' requested here 1043 | return loadContigs(store, fileNames, true); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:5: note: in instantiation of function template specialization 'seqan::loadContigs, seqan::StringSet>>' requested here 792 | loadContigs(fragmentStore1, genomeFileNameList); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:596:12: note: (skipping 14 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 596 | return open(stream, fileStream, stream.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:296:5: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>>' requested here 296 | readRecord(meta, seq, file, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1014:17: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>>' requested here 1014 | readRecord(meta, contig.seq, seqFile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:12: note: in instantiation of function template specialization 'seqan::loadContigs>' requested here 1043 | return loadContigs(store, fileNames, true); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:5: note: in instantiation of function template specialization 'seqan::loadContigs, seqan::StringSet>>' requested here 792 | loadContigs(fragmentStore1, genomeFileNameList); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:88: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: 'binary_function, seqan::GapAnchor, bool>' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:359:9: note: in instantiation of template class 'seqan::_LessGapAnchor, const seqan::Tag>' requested here 359 | _LessGapAnchor::Type, SortGapPos const>() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:662:28: note: in instantiation of function template specialization 'seqan::upperBoundGapAnchor>, int>' requested here 662 | me.anchorIdx = upperBoundGapAnchor(anchors, pos, SortGapPos()) - begin(anchors, Standard()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:93:9: note: in instantiation of function template specialization 'seqan::_goToGapAnchorIterator>, seqan::AnchorGaps>>>, seqan::GapsIterator>>>>, int>' requested here 93 | _goToGapAnchorIterator(*this, data_container->data_viewCutBegin + data_container->data_cutBegin); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:523:12: note: in instantiation of member function 'seqan::Iter>, seqan::AnchorGaps>>>, seqan::GapsIterator>>>>::Iter' requested here 523 | return typename Iterator > >::Type(me); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:362:12: note: in instantiation of function template specialization 'seqan::begin>, seqan::String>>' requested here 362 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:639:41: note: in instantiation of function template specialization 'seqan::begin>, seqan::AnchorGaps>>>>' requested here 639 | typename Iterator::Type it = begin(gaps); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:699:13: note: in instantiation of function template specialization 'seqan::cigarToGapAnchorRead>, seqan::AnchorGaps>>>, seqan::String>>' requested here 699 | cigarToGapAnchorRead(readGaps, record.cigar); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:687:26: note: in instantiation of function template specialization 'readMatchesFromSamBam>>, seqan::FormattedFile, seqan::Tag>, seqan::FragmentStore, int, long, SNPCallingOptions>' requested here 687 | int result = readMatchesFromSamBam(setContigAnchorGaps, *bamFileIns[j], records[j], fragmentStoreTmp, fragmentStore1, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:13: note: in instantiation of function template specialization 'detectSNPsForContig, seqan::Tag> *>, std::vector, seqan::String>>, SNPCallingOptions, MethCallingOptions>' requested here 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::GapAnchor, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:81:23: warning: 'binary_function>, seqan::AlignQualityStoreElement, bool>' is deprecated [-Wdeprecated-declarations] 81 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:244:21: note: in instantiation of template class 'LessGStackOaMQ>>, seqan::String>>' requested here 244 | LessGStackOaMQ(fragmentStore.alignQualityStore)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:702:17: note: in instantiation of function template specialization 'applyPileupCorrection, unsigned int, SNPCallingOptions>' requested here 702 | applyPileupCorrection(fragmentStoreTmp,sizeBefore,(unsigned)length(fragmentStoreTmp.alignedReadStore),options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:13: note: in instantiation of function template specialization 'detectSNPsForContig, seqan::Tag> *>, std::vector, seqan::String>>, SNPCallingOptions, MethCallingOptions>' requested here 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::AlignQualityStoreElement, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:17:23: warning: 'binary_function>, seqan::AlignQualityStoreElement, bool>' is deprecated [-Wdeprecated-declarations] 17 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:248:21: note: in instantiation of template class 'LessGStackMQ>>, seqan::String>>' requested here 248 | LessGStackMQ(fragmentStore.alignQualityStore)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:702:17: note: in instantiation of function template specialization 'applyPileupCorrection, unsigned int, SNPCallingOptions>' requested here 702 | applyPileupCorrection(fragmentStoreTmp,sizeBefore,(unsigned)length(fragmentStoreTmp.alignedReadStore),options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:13: note: in instantiation of function template specialization 'detectSNPsForContig, seqan::Tag> *>, std::vector, seqan::String>>, SNPCallingOptions, MethCallingOptions>' requested here 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::AlignQualityStoreElement, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:142:37: warning: 'binary_function>, seqan::AlignedReadStoreElement>, bool>' is deprecated [-Wdeprecated-declarations] 142 | struct LessGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:155:117: note: in instantiation of template class 'LessGPos>>' requested here 155 | ::std::sort(begin(fragmentStore.alignedReadStore, Standard()), end(fragmentStore.alignedReadStore, Standard()), LessGPos()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:728:17: note: in instantiation of function template specialization 'copyNextWindowMatchesAndReads, seqan::String>>, int, long, SNPCallingOptions>' requested here 728 | copyNextWindowMatchesAndReads(fragmentStoreTmp, setContigAnchorGaps, tmpReads, tmpRs, tmpMatches, tmpQualities, tmpSetContigAnchorGaps, currContigId, currentWindowEnd, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:13: note: in instantiation of function template specialization 'detectSNPsForContig, seqan::Tag> *>, std::vector, seqan::String>>, SNPCallingOptions, MethCallingOptions>' requested here 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::AlignedReadStoreElement>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:88: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: 'binary_function, seqan::GapAnchor, bool>' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:327:9: note: in instantiation of template class 'seqan::_LessGapAnchor, const seqan::Tag>' requested here 327 | _LessGapAnchor::Type, SortSeqPos const>() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:848:25: note: in instantiation of function template specialization 'seqan::upperBoundGapAnchor>, unsigned long>' requested here 848 | anchorIdx = upperBoundGapAnchor(anchors, pos, SortSeqPos()) - begin(anchors, Standard()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1158:37: note: in instantiation of function template specialization 'seqan::positionSeqToGap>, seqan::String>, unsigned long>' requested here 1158 | TContigPos maxPos = positionSeqToGap(contigGaps,length(fragStoreGroup.contigStore[0].seq)-1)+1; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:17: note: in instantiation of function template specialization 'doCheckRealignCall, long, seqan::String>>, seqan::FormattedFile, seqan::Tag>, seqan::FormattedFile, seqan::Tag>, MethCallingOptions, SNPCallingOptions>' requested here 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:13: note: in instantiation of function template specialization 'detectSNPsForContig, seqan::Tag> *>, std::vector, seqan::String>>, SNPCallingOptions, MethCallingOptions>' requested here 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::GapAnchor, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:60: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: 'binary_function>, seqan::AlignedReadStoreElement>, bool>' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:491:9: note: in instantiation of template class 'seqan::_LessAlignedRead>, const seqan::Tag>' requested here 491 | _LessAlignedRead::Type, Tag const>() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1568:5: note: in instantiation of function template specialization 'seqan::sortAlignedReads>>, seqan::SortBeginPos_>' requested here 1568 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1162:17: note: in instantiation of function template specialization 'seqan::layoutAlignment>' requested here 1162 | layoutAlignment(layout, fragStoreGroup); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:17: note: in instantiation of function template specialization 'doCheckRealignCall, long, seqan::String>>, seqan::FormattedFile, seqan::Tag>, seqan::FormattedFile, seqan::Tag>, MethCallingOptions, SNPCallingOptions>' requested here 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:13: note: in instantiation of function template specialization 'detectSNPsForContig, seqan::Tag> *>, std::vector, seqan::String>>, SNPCallingOptions, MethCallingOptions>' requested here 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::AlignedReadStoreElement>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:60: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: 'binary_function>, seqan::AlignedReadStoreElement>, bool>' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:491:9: note: in instantiation of template class 'seqan::_LessAlignedRead>, const seqan::Tag>' requested here 491 | _LessAlignedRead::Type, Tag const>() ); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1569:5: note: in instantiation of function template specialization 'seqan::sortAlignedReads>>, seqan::SortContigId_>' requested here 1569 | sortAlignedReads(store.alignedReadStore, SortContigId()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1162:17: note: in instantiation of function template specialization 'seqan::layoutAlignment>' requested here 1162 | layoutAlignment(layout, fragStoreGroup); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:17: note: in instantiation of function template specialization 'doCheckRealignCall, long, seqan::String>>, seqan::FormattedFile, seqan::Tag>, seqan::FormattedFile, seqan::Tag>, MethCallingOptions, SNPCallingOptions>' requested here 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:13: note: in instantiation of function template specialization 'detectSNPsForContig, seqan::Tag> *>, std::vector, seqan::String>>, SNPCallingOptions, MethCallingOptions>' requested here 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::AlignedReadStoreElement>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:44: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:62: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: 'binary_function>, seqan::AlignedReadStoreElement>, bool>' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2363:58: note: in instantiation of template class 'seqan::LessConvertPairWiseToGlobalAlignment>' requested here 2363 | LessConvertPairWiseToGlobalAlignment lessFunctor(store, offsetRecord); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:751:17: note: in instantiation of function template specialization 'seqan::convertPairWiseToGlobalAlignment, seqan::String>>>' requested here 751 | convertPairWiseToGlobalAlignment(fragmentStoreTmp, setContigAnchorGaps); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:13: note: in instantiation of function template specialization 'detectSNPsForContig, seqan::Tag> *>, std::vector, seqan::String>>, SNPCallingOptions, MethCallingOptions>' requested here 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::AlignedReadStoreElement>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment, seqan::PrefixSegment>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:471:12: note: in implicit copy constructor for 'seqan::Segment, seqan::PrefixSegment>' first required here 471 | return typename Prefix::Type(t, pos_end); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_utils.h:125:12: note: in instantiation of function template specialization 'seqan::prefix, unsigned long>' requested here 125 | return prefix(lhs, rhsLen) == rhs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/vcf_io/read_vcf.h:141:18: note: in instantiation of function template specialization 'seqan::startsWith, char[6]>' requested here 141 | if (!startsWith(buffer, "CHROM")) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/vcf_io/vcf_file.h:198:5: note: in instantiation of function template specialization 'seqan::readHeader>, seqan::StreamIterator>>, seqan::StringSet>, seqan::NameStoreCache>>, seqan::Dependent<>>' requested here 198 | readHeader(header, context(file), file.iter, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:953:9: note: in instantiation of function template specialization 'seqan::readHeader' requested here 953 | readHeader(vcfHeader, vcfFileIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Bed_>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:968:14: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 968 | if (!open(bedFileIn, toCString(contigTempFileNamesBed[i]))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:18: note: in instantiation of function template specialization 'detectSNPs' requested here 1265 | int result = detectSNPs(options, methOptions); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ 39 warnings generated. [ 45% 64/141] /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o -MF apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o.d -o apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp FAILED: [code=1] apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o /usr/local/libexec/ccache/c++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o -MF apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o.d -o apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:116: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel.h:92: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable] 69 | unsigned count = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: 'unary_function, seqan::SimpleType>' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::SimpleType>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:102: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/iostream_zip_impl.h:132:44: warning: variable 'total_written_byte_size' set but not used [-Wunused-but-set-variable] 132 | std::streamsize written_byte_size = 0, total_written_byte_size = 0; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable] 125 | for (unsigned row = 0; !atEnd(reader); ++row) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:120: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:71: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/argument_parser.h:43: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] 454 | if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | && /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_version_check.h:454:9: note: cast one or both operands to int to silence this warning /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1654:42: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 1654 | struct LessPositionOverlap : public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1725:35: note: in instantiation of template class 'LessPositionOverlap' requested here 1725 | sort(possibleCorrections, LessPositionOverlap(), Parallel()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1636:34: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 1636 | struct LessOverlap : public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1775:35: note: in instantiation of template class 'LessOverlap' requested here 1775 | sort(possibleCorrections, LessOverlap(), Parallel()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4671:2: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 4671 | String superPackages; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4667:5: note: previous statement is here 4667 | for (int i = 0; i < (int)dirLen; ++i) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:115: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:115: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Raw_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>>' requested here 565 | return guessFormatFromStream(file.stream, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: note: in instantiation of function template specialization 'seqan::guessFormat, void>' requested here 712 | if (!guessFormat(file)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:14: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 578 | if (!open(seqFile, toCString(fileName))) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:10: note: in instantiation of function template specialization 'seqan::loadReadsNoNames>' requested here 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:45: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:43: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:596:12: note: (skipping 12 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 596 | return open(stream, fileStream, stream.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:231:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here 231 | readRecord(meta, seq, file, static_cast::Base const & >(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:231:9: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:296:5: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>, seqan::FormattedFile, seqan::Tag>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>>>' requested here 296 | readRecord(meta, seq, file, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:591:13: note: in instantiation of function template specialization 'seqan::readRecord, seqan::String>>' requested here 591 | readRecord(_id, seq, seqFile); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:10: note: in instantiation of function template specialization 'seqan::loadReadsNoNames>' requested here 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:114: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: 'binary_function>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::Pair>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7NCompMulti>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1042:26: note: in instantiation of template class 'seqan::Pool>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>' requested here 1042 | typedef typename Pool< TValue, TSpec >::SizeType Type; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:52:22: note: in instantiation of template class 'seqan::Size>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>>' requested here 52 | typename Size::Type, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:236:73: note: in instantiation of template class 'seqan::Value>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Namer>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>>>>' requested here 236 | typedef _skew7GlobalSlicedMulti func_slice_t; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:41:40: note: expanded from macro 'TypeOf_' 41 | #define TypeOf_(TObject) typename Value::Type | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of template class 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::Pair>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:114: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: 'unary_function>, unsigned long, seqan::Tag>, seqan::Pair>>' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:78:26: note: in instantiation of template class 'seqan::_skew7GlobalSlicedMulti>, unsigned long, seqan::Tag>, seqan::String, unsigned long>' requested here 78 | typedef typename TFunctor::result_type Type; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:239:23: note: in instantiation of template class 'seqan::Value>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Namer>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>>>, seqan::Filter>, unsigned long, seqan::Tag>, seqan::String, unsigned long>>>>' requested here 239 | typedef Pool< TypeOf_(TSlicedPos), MapperSpec< MapperConfigSize< filterI1, TSizeOf_(TSlicedPos) > > > TNames_Sliced; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:41:40: note: expanded from macro 'TypeOf_' 41 | #define TypeOf_(TObject) typename Value::Type | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of template class 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayPipelining> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayWrapper> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 198 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:614:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 614 | createSuffixArray(indexSA(index), indexText(index), alg); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, unsigned long, seqan::Tag>, seqan::Pair>>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: 'unary_function>, unsigned long>' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::filterI1>>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1042:26: note: in instantiation of template class 'seqan::Pool>, seqan::MapperSpec>>, unsigned long>>>' requested here 1042 | typedef typename Pool< TValue, TSpec >::SizeType Type; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:309:26: note: in instantiation of template class 'seqan::Size>, seqan::MapperSpec>>, unsigned long>>>>' requested here 309 | typedef typename Size::Type Type; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:220:16: note: in instantiation of template class 'seqan::Size>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>>' requested here 220 | public Size {}; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_counter.h:49:22: note: in instantiation of template class 'seqan::Value>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>>' requested here 49 | typename Value::Type, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:252:23: note: (skipping 7 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 252 | typedef Pool< TypeOf_(TRenamer), MapperSpec< MapperConfigSize< filterI1, TSizeOf_(TRenamer) > > > TNames_Linear; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:41:40: note: expanded from macro 'TypeOf_' 41 | #define TypeOf_(TObject) typename Value::Type | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:270:30: note: in instantiation of template class 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>' requested here 270 | TSorterS0 sortedS0; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of template class 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayPipelining> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayWrapper> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 198 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:614:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 614 | createSuffixArray(indexSA(index), indexText(index), alg); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:271:30: note: in instantiation of template class 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>' requested here 271 | TSorterS3 sortedS3; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of template class 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayPipelining> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayWrapper> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 198 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:614:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 614 | createSuffixArray(indexSA(index), indexText(index), alg); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:272:30: note: in instantiation of template class 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>' requested here 272 | TSorterS5 sortedS5; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of template class 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayPipelining> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayWrapper> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 198 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:614:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 614 | createSuffixArray(indexSA(index), indexText(index), alg); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:273:30: note: in instantiation of template class 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>' requested here 273 | TSorterS6 sortedS6; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of template class 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayPipelining> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayWrapper> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 198 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:614:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 614 | createSuffixArray(indexSA(index), indexText(index), alg); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: 'unary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, unsigned long>' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7NMapExtended>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:274:32: note: in instantiation of template class 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::MapperSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>' requested here 274 | TSorterS124 sortedS124; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of template class 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayPipelining> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayWrapper> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 198 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:614:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 614 | createSuffixArray(indexSA(index), indexText(index), alg); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:110: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, seqan::SkewDCStream>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:360:55: note: in instantiation of template class 'seqan::CompareSkewDCStream>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>' requested here 360 | CompareSkewDCStream streamGreater; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:275:32: note: in instantiation of template class 'seqan::Pipe>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Pool>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Pool>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Pool>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Pool>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::MapperSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>>, seqan::Merger7Multi>>' requested here 275 | TMerger in; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of template class 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayPipelining> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayWrapper> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 198 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:614:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 614 | createSuffixArray(indexSA(index), indexText(index), alg); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, seqan::SkewDCStream>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: 'unary_function>, unsigned long>' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:103:21: note: in instantiation of template class 'seqan::filterI2>>' requested here 103 | TFunctor F; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:361:45: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>' requested here 361 | TFilter filter(names_sliced); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::process>>>, seqan::Source<>>, seqan::Caster>>>' requested here 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::Pipe>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: in instantiation of function template specialization 'seqan::_createSuffixArrayPipelining> *>, seqan::String>, seqan::Owner<>, seqan::Skew7>' requested here 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:9: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 198 | _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_::Type()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: 'binary_function>, seqan::Tag>, seqan::Pair>, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7NComp>, seqan::Tag>>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1042:26: note: in instantiation of template class 'seqan::Pool>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>' requested here 1042 | typedef typename Pool< TValue, TSpec >::SizeType Type; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:52:22: note: in instantiation of template class 'seqan::Size>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>>' requested here 52 | typename Size::Type, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:260:66: note: in instantiation of template class 'seqan::Value>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Namer>, seqan::Tag>>>>>' requested here 260 | typedef _skew7NMapSliced nmap_sliced_t; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:41:40: note: expanded from macro 'TypeOf_' 41 | #define TypeOf_(TObject) typename Value::Type | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: (skipping 7 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tag>, seqan::Pair>, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: 'unary_function>, unsigned long>' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7NMapSliced>>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1042:26: note: in instantiation of template class 'seqan::Pool>, seqan::MapperSpec>>, unsigned long>>>' requested here 1042 | typedef typename Pool< TValue, TSpec >::SizeType Type; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:265:92: note: in instantiation of template class 'seqan::Size>, seqan::MapperSpec>>, unsigned long>>>>' requested here 265 | typedef Pool< TypeOf_(TNames_Sliced), MapperSpec< MapperConfigSize< nmap_linear_t, TSizeOf_(TNames_Sliced) > > > TNames_Linear_Unique; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:42:40: note: expanded from macro 'TSizeOf_' 42 | #define TSizeOf_(TObject) typename Size::Type | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::process>>>, seqan::Source<>>, seqan::Caster>>>' requested here 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: (skipping 6 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:78:26: note: in instantiation of template class 'seqan::_skew7UnslicerFunc' requested here 78 | typedef typename TFunctor::result_type Type; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_counter.h:49:22: note: in instantiation of template class 'seqan::Value>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew3>, seqan::Filter>>>' requested here 49 | typename Value::Type, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:281:23: note: in instantiation of template class 'seqan::Value>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew3>, seqan::Filter>>, seqan::Counter>>' requested here 281 | typedef Pool< TypeOf_(TRenamer), MapperSpec< MapperConfigSize< nmap_linear_t, TSizeOf_(TRenamer) > > > TNames_Linear; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:41:40: note: expanded from macro 'TypeOf_' 41 | #define TypeOf_(TObject) typename Value::Type | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::process>>>, seqan::Source<>>, seqan::Caster>>>' requested here 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: (skipping 6 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 3>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:299:21: note: in instantiation of template class 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>' requested here 299 | TSorterS0 sortedS0; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::process>>>, seqan::Source<>>, seqan::Caster>>>' requested here 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::Pipe>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 1>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:300:21: note: in instantiation of template class 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>' requested here 300 | TSorterS3 sortedS3; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::process>>>, seqan::Source<>>, seqan::Caster>>>' requested here 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::Pipe>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 1>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:301:21: note: in instantiation of template class 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>' requested here 301 | TSorterS5 sortedS5; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::process>>>, seqan::Source<>>, seqan::Caster>>>' requested here 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::Pipe>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 2>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:302:21: note: in instantiation of template class 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>' requested here 302 | TSorterS6 sortedS6; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::process>>>, seqan::Source<>>, seqan::Caster>>>' requested here 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::Pipe>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: 'unary_function, seqan::Tuple>, seqan::Tag>, unsigned long>' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew7NMapExtended, seqan::Tuple>, seqan::Tag>>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:303:21: note: in instantiation of template class 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::MapperSpec, seqan::Tuple>, seqan::Tag>>, unsigned long>>>' requested here 303 | TSorterS124 sortedS124; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::process>>>, seqan::Source<>>, seqan::Caster>>>' requested here 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::Pipe>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::Tuple>, seqan::Tag>, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:110: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: 'binary_function, seqan::Tuple>, seqan::Tag>>, seqan::SkewDCStream, seqan::Tuple>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:215:55: note: in instantiation of template class 'seqan::CompareSkewDCStream, seqan::Tuple>, seqan::Tag>>' requested here 215 | CompareSkewDCStream streamGreater; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:304:21: note: in instantiation of template class 'seqan::Pipe, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::MapperSpec, seqan::Tuple>, seqan::Tag>>, unsigned long>>>>, seqan::Merger7>' requested here 304 | TMerger in; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::process>>>, seqan::Source<>>, seqan::Caster>>>' requested here 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::Pipe>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>>, seqan::SkewDCStream, seqan::Tuple>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, seqan::PageBucket>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::_skew7NCompMulti>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, seqan::MergeStreamComparer>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::_skew7NCompMulti>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:920:33: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 920 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:785:13: note: in instantiation of member function 'seqan::Pool>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>::endRead' requested here 785 | endRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:313:41: note: (skipping 8 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 313 | TSortTuples sorter; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, seqan::PageBucket>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::Pair>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterConfigSize>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:25: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 904 | writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: note: (skipping 9 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 786 | endWrite(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::Pair>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: 'unary_function>>, void>' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:473:17: note: in instantiation of member class 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>::insertBucket' requested here 473 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:899:25: note: in instantiation of member function 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::Tag>, seqan::MapperMemAdapter>, seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>>, seqan::Tag>::begin' requested here 899 | writer->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1243:23: note: in instantiation of member function 'seqan::Pool>, seqan::MapperSpec>>, unsigned long>>>::beginWrite' requested here 1243 | return me.beginWrite(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:16: note: in instantiation of function template specialization 'seqan::beginWrite>, seqan::MapperSpec>>, unsigned long>>>' requested here 1369 | return beginWrite(dest) && append(dest, src) && endWrite(dest); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:16: note: (skipping 9 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1376 | return assign(dest, src); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:135:14: note: in instantiation of function template specialization 'seqan::control>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>' requested here 135 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:507:16: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 507 | return control(me.in, command); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, seqan::Tuple, 7, seqan::BitPacked<>>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, seqan::PageBucket>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, seqan::MergeStreamComparer>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:949:33: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 949 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: in instantiation of member function 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>::_freeHandlers' requested here 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1109:12: note: (skipping 10 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1109 | me.resize(new_length); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, seqan::PageBucket>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterConfigSize>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:950:33: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 950 | if (writer) writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:114: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:98: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: warning: definition of implicit copy assignment operator for 'Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 82 | inline Triple(Triple const &_p) | ^ /usr/include/c++/v1/__algorithm/sift_down.h:61:14: note: in implicit copy assignment operator for 'seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>' first required here 61 | *__start = _Ops::__iter_move(__child_i); | ^ /usr/include/c++/v1/__algorithm/make_heap.h:39:12: note: in instantiation of function template specialization 'std::__sift_down>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>> &, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag> *>' requested here 39 | std::__sift_down<_AlgPolicy>(__first, __comp_ref, __n, __first + __start); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:41:8: note: in instantiation of function template specialization 'std::__make_heap>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>> &, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag> *>' requested here 41 | std::__make_heap<_AlgPolicy>(__first, __middle, __comp); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:65:12: note: in instantiation of function template specialization 'std::__partial_sort_impl>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>> &, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag> *, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag> *>' requested here 65 | std::__partial_sort_impl<_AlgPolicy>(__first, __middle, __last, static_cast<__comp_ref_type<_Compare> >(__comp)); | ^ /usr/include/c++/v1/__algorithm/sort.h:992:10: note: in instantiation of function template specialization 'std::__partial_sort>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag> *, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag> *>' requested here 992 | std::__partial_sort<_AlgPolicy>( | ^ /usr/include/c++/v1/__algorithm/sort.h:1003:8: note: (skipping 17 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1003 | std::__sort_impl<_ClassicAlgPolicy>(std::move(__first), std::move(__last), __comp); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, seqan::PageBucket>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, seqan::MergeStreamComparer>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:949:33: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 949 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: in instantiation of member function 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>::_freeHandlers' requested here 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1109:12: note: (skipping 10 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1109 | me.resize(new_length); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, seqan::PageBucket>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterConfigSize>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:950:33: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 950 | if (writer) writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>>, seqan::PageBucket>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>>, seqan::MergeStreamComparer>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:949:33: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 949 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: in instantiation of member function 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>::_freeHandlers' requested here 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1109:12: note: (skipping 10 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1109 | me.resize(new_length); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>>, seqan::PageBucket>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterConfigSize>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:950:33: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 950 | if (writer) writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:114: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:98: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: warning: definition of implicit copy assignment operator for 'Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 82 | inline Triple(Triple const &_p) | ^ /usr/include/c++/v1/__algorithm/sift_down.h:61:14: note: in implicit copy assignment operator for 'seqan::Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>' first required here 61 | *__start = _Ops::__iter_move(__child_i); | ^ /usr/include/c++/v1/__algorithm/make_heap.h:39:12: note: in instantiation of function template specialization 'std::__sift_down>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>> &, seqan::Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag> *>' requested here 39 | std::__sift_down<_AlgPolicy>(__first, __comp_ref, __n, __first + __start); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:41:8: note: in instantiation of function template specialization 'std::__make_heap>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>> &, seqan::Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag> *>' requested here 41 | std::__make_heap<_AlgPolicy>(__first, __middle, __comp); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:65:12: note: in instantiation of function template specialization 'std::__partial_sort_impl>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>> &, seqan::Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag> *, seqan::Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag> *>' requested here 65 | std::__partial_sort_impl<_AlgPolicy>(__first, __middle, __last, static_cast<__comp_ref_type<_Compare> >(__comp)); | ^ /usr/include/c++/v1/__algorithm/sort.h:992:10: note: in instantiation of function template specialization 'std::__partial_sort>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag> *, seqan::Triple>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag> *>' requested here 992 | std::__partial_sort<_AlgPolicy>( | ^ /usr/include/c++/v1/__algorithm/sort.h:1003:8: note: (skipping 17 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1003 | std::__sort_impl<_ClassicAlgPolicy>(std::move(__first), std::move(__last), __comp); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>>, seqan::PageBucket>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>>, seqan::MergeStreamComparer>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::_skew7ExtendComp>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:949:33: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 949 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: in instantiation of member function 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>::_freeHandlers' requested here 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1109:12: note: (skipping 10 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1109 | me.resize(new_length); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>>, seqan::PageBucket>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterConfigSize>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:950:33: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 950 | if (writer) writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:114: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:98: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: warning: definition of implicit copy assignment operator for 'Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 82 | inline Triple(Triple const &_p) | ^ /usr/include/c++/v1/__algorithm/sift_down.h:61:14: note: in implicit copy assignment operator for 'seqan::Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>' first required here 61 | *__start = _Ops::__iter_move(__child_i); | ^ /usr/include/c++/v1/__algorithm/make_heap.h:39:12: note: in instantiation of function template specialization 'std::__sift_down>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>> &, seqan::Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag> *>' requested here 39 | std::__sift_down<_AlgPolicy>(__first, __comp_ref, __n, __first + __start); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:41:8: note: in instantiation of function template specialization 'std::__make_heap>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>> &, seqan::Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag> *>' requested here 41 | std::__make_heap<_AlgPolicy>(__first, __middle, __comp); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:65:12: note: in instantiation of function template specialization 'std::__partial_sort_impl>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>> &, seqan::Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag> *, seqan::Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag> *>' requested here 65 | std::__partial_sort_impl<_AlgPolicy>(__first, __middle, __last, static_cast<__comp_ref_type<_Compare> >(__comp)); | ^ /usr/include/c++/v1/__algorithm/sort.h:992:10: note: in instantiation of function template specialization 'std::__partial_sort>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>>, seqan::Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag> *, seqan::Triple>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag> *>' requested here 992 | std::__partial_sort<_AlgPolicy>( | ^ /usr/include/c++/v1/__algorithm/sort.h:1003:8: note: (skipping 17 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1003 | std::__sort_impl<_ClassicAlgPolicy>(std::move(__first), std::move(__last), __comp); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: 'unary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:473:17: note: in instantiation of member class 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::MapperSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::MapperAsyncWriter>::insertBucket' requested here 473 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::MapperSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::MapperAsyncWriter>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:899:25: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::MapperSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::MapperMemAdapter>, seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::MapperSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>, seqan::MapperAsyncWriter>>, seqan::Tag>::begin' requested here 899 | writer->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1243:23: note: in instantiation of member function 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::MapperSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>::beginWrite' requested here 1243 | return me.beginWrite(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:342:13: note: in instantiation of function template specialization 'seqan::beginWrite>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::MapperSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, unsigned long>>>' requested here 342 | beginWrite(out124))) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:17: note: (skipping 8 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 350 | _skew7ExtendMulti( | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:111: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: 'unary_function>, unsigned long>' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:340:41: note: in instantiation of template class 'seqan::_skew7NMapLinear>>' requested here 340 | nmap_linear_t map_linear(length(namer)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:13: note: in instantiation of function template specialization 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>::process>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>>' requested here 312 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of member function 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>::Pipe' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::process>>>, seqan::Source<>>, seqan::Caster>>>' requested here 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: note: in instantiation of function template specialization 'seqan::Pipe>>>, seqan::Source<>>, seqan::Caster>>, seqan::Multi>, seqan::String>>::Pipe>' requested here 107 | creator_t creator(unsigner, stringSetLimits(stringSet)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:9: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 173 | _createSuffixArrayPipelining(sa, s, Skew7()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:107: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: 'binary_function>, seqan::Tag>, seqan::Pair>, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew3NComp>, seqan::Tag>>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1042:26: note: in instantiation of template class 'seqan::Pool>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>' requested here 1042 | typedef typename Pool< TValue, TSpec >::SizeType Type; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:52:22: note: in instantiation of template class 'seqan::Size>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>>' requested here 52 | typename Size::Type, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:183:66: note: in instantiation of template class 'seqan::Value>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Namer>, seqan::Tag>>>>>' requested here 183 | typedef _skew3NMapSliced nmap_sliced_t; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:41:40: note: expanded from macro 'TypeOf_' 41 | #define TypeOf_(TObject) typename Value::Type | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew3>' requested here 376 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:13: note: (skipping 9 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 312 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tag>, seqan::Pair>, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:107: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: 'unary_function>, unsigned long>' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew3NMapSliced>>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1042:26: note: in instantiation of template class 'seqan::Pool>, seqan::MapperSpec>>, unsigned long>>>' requested here 1042 | typedef typename Pool< TValue, TSpec >::SizeType Type; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:188:92: note: in instantiation of template class 'seqan::Size>, seqan::MapperSpec>>, unsigned long>>>>' requested here 188 | typedef Pool< TypeOf_(TNames_Sliced), MapperSpec< MapperConfigSize< nmap_linear_t, TSizeOf_(TNames_Sliced) > > > TNames_Linear_Unique; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:42:40: note: expanded from macro 'TSizeOf_' 42 | #define TSizeOf_(TObject) typename Size::Type | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew3>' requested here 376 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:13: note: in instantiation of function template specialization 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>::process>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>>' requested here 312 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: (skipping 8 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:107: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:78:26: note: in instantiation of template class 'seqan::_skew3UnslicerFunc' requested here 78 | typedef typename TFunctor::result_type Type; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_counter.h:49:22: note: in instantiation of template class 'seqan::Value>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew3>, seqan::Filter>>>' requested here 49 | typename Value::Type, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:196:23: note: in instantiation of template class 'seqan::Value>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew3>, seqan::Filter>>, seqan::Counter>>' requested here 196 | typedef Pool< TypeOf_(TRenamer), MapperSpec< MapperConfigSize< nmap_linear_t, TSizeOf_(TRenamer) > > > TNames_Linear; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:41:40: note: expanded from macro 'TypeOf_' 41 | #define TypeOf_(TObject) typename Value::Type | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew3>' requested here 376 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:13: note: in instantiation of function template specialization 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>::process>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>>' requested here 312 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: (skipping 8 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:107: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: 'binary_function, seqan::Tuple, seqan::Tag>, seqan::Triple, seqan::Tuple, seqan::Tag>, int>' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew3ExtendComp, seqan::Tuple, seqan::Tag>>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:208:21: note: in instantiation of template class 'seqan::Pool, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>' requested here 208 | TSorterS0 sortedS0; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew3>' requested here 376 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:13: note: in instantiation of function template specialization 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>::process>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>>' requested here 312 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of member function 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>::Pipe' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: (skipping 7 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple, seqan::Tag>, seqan::Triple, seqan::Tuple, seqan::Tag>, int>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:107: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: 'unary_function, seqan::Tuple, seqan::Tag>, unsigned long>' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:708:29: note: in instantiation of template class 'seqan::_skew3NMapExtended, seqan::Tuple, seqan::Tag>>' requested here 708 | HandlerArgs handlerArgs; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:209:21: note: in instantiation of template class 'seqan::Pool, seqan::Tuple, seqan::Tag>, seqan::MapperSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>' requested here 209 | TSorterS12 sortedS12; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: note: in instantiation of template class 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew3>' requested here 376 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:13: note: in instantiation of function template specialization 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>::process>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>>' requested here 312 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of member function 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>::Pipe' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: (skipping 7 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::Tuple, seqan::Tag>, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function>, seqan::Tag>>, seqan::PageBucket>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer>, seqan::Tag>, seqan::_skew7NComp>, seqan::Tag>>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType>, seqan::Tag>>, seqan::MergeStreamComparer>, seqan::Tag>, seqan::_skew7NComp>, seqan::Tag>>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:920:33: note: in instantiation of member function 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 920 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:785:13: note: in instantiation of member function 'seqan::Pool>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>::endRead' requested here 785 | endRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:331:41: note: (skipping 10 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 331 | TSortTuples sorter; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tag>>, seqan::PageBucket>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function>, seqan::Tag>, seqan::Pair>, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less>, seqan::Tag>>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer>, seqan::Tag>, seqan::SorterConfigSize>, seqan::Tag>>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:25: note: in instantiation of member function 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 904 | writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 786 | endWrite(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tag>, seqan::Pair>, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: 'unary_function>>, void>' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:473:17: note: in instantiation of member class 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>::insertBucket' requested here 473 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:899:25: note: in instantiation of member function 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::Tag>, seqan::MapperMemAdapter>, seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>>, seqan::Tag>::begin' requested here 899 | writer->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1243:23: note: in instantiation of member function 'seqan::Pool>, seqan::MapperSpec>>, unsigned long>>>::beginWrite' requested here 1243 | return me.beginWrite(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:16: note: in instantiation of function template specialization 'seqan::beginWrite>, seqan::MapperSpec>>, unsigned long>>>' requested here 1369 | return beginWrite(dest) && append(dest, src) && endWrite(dest); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:16: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1376 | return assign(dest, src); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:135:14: note: in instantiation of function template specialization 'seqan::control>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>' requested here 135 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:547:16: note: (skipping 14 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 547 | return control(me, ControlBeginRead()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: 'unary_function>>, void>' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:473:17: note: in instantiation of member class 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>::insertBucket' requested here 473 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:899:25: note: in instantiation of member function 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::Tag>, seqan::MapperMemAdapter>, seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>>, seqan::Tag>::begin' requested here 899 | writer->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1243:23: note: in instantiation of member function 'seqan::Pool>, seqan::MapperSpec>>, unsigned long>>>::beginWrite' requested here 1243 | return me.beginWrite(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:16: note: in instantiation of function template specialization 'seqan::beginWrite>, seqan::MapperSpec>>, unsigned long>>>' requested here 1369 | return beginWrite(dest) && append(dest, src) && endWrite(dest); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:16: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1376 | return assign(dest, src); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function, seqan::Tuple>, seqan::Tag>>, seqan::PageBucket, seqan::Tuple>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer, seqan::Tuple>, seqan::Tag>, seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 3>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType, seqan::Tuple>, seqan::Tag>>, seqan::MergeStreamComparer, seqan::Tuple>, seqan::Tag>, seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 3>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:949:33: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 949 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: in instantiation of member function 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>::_freeHandlers' requested here 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1109:12: note: (skipping 12 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1109 | me.resize(new_length); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>>, seqan::PageBucket, seqan::Tuple>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less, seqan::Tuple>, seqan::Tag>, 3>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer, seqan::Tuple>, seqan::Tag>, seqan::SorterConfigSize, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:950:33: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 950 | if (writer) writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:114: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:98: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: warning: definition of implicit copy assignment operator for 'Triple, seqan::Tuple>, seqan::Tag>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 82 | inline Triple(Triple const &_p) | ^ /usr/include/c++/v1/__algorithm/sift_down.h:61:14: note: in implicit copy assignment operator for 'seqan::Triple, seqan::Tuple>, seqan::Tag>' first required here 61 | *__start = _Ops::__iter_move(__child_i); | ^ /usr/include/c++/v1/__algorithm/make_heap.h:39:12: note: in instantiation of function template specialization 'std::__sift_down, seqan::Tuple>, seqan::Tag>, 3>> &, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 39 | std::__sift_down<_AlgPolicy>(__first, __comp_ref, __n, __first + __start); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:41:8: note: in instantiation of function template specialization 'std::__make_heap, seqan::Tuple>, seqan::Tag>, 3>> &, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 41 | std::__make_heap<_AlgPolicy>(__first, __middle, __comp); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:65:12: note: in instantiation of function template specialization 'std::__partial_sort_impl, seqan::Tuple>, seqan::Tag>, 3>> &, seqan::Triple, seqan::Tuple>, seqan::Tag> *, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 65 | std::__partial_sort_impl<_AlgPolicy>(__first, __middle, __last, static_cast<__comp_ref_type<_Compare> >(__comp)); | ^ /usr/include/c++/v1/__algorithm/sort.h:992:10: note: in instantiation of function template specialization 'std::__partial_sort, seqan::Tuple>, seqan::Tag>, 3>>, seqan::Triple, seqan::Tuple>, seqan::Tag> *, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 992 | std::__partial_sort<_AlgPolicy>( | ^ /usr/include/c++/v1/__algorithm/sort.h:1003:8: note: (skipping 19 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1003 | std::__sort_impl<_ClassicAlgPolicy>(std::move(__first), std::move(__last), __comp); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function, seqan::Tuple>, seqan::Tag>>, seqan::PageBucket, seqan::Tuple>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer, seqan::Tuple>, seqan::Tag>, seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 1>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType, seqan::Tuple>, seqan::Tag>>, seqan::MergeStreamComparer, seqan::Tuple>, seqan::Tag>, seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 1>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:949:33: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 949 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: in instantiation of member function 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>::_freeHandlers' requested here 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1109:12: note: (skipping 12 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1109 | me.resize(new_length); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>>, seqan::PageBucket, seqan::Tuple>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less, seqan::Tuple>, seqan::Tag>, 1>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer, seqan::Tuple>, seqan::Tag>, seqan::SorterConfigSize, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:950:33: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 950 | if (writer) writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function, seqan::Tuple>, seqan::Tag>>, seqan::PageBucket, seqan::Tuple>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer, seqan::Tuple>, seqan::Tag>, seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 1>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType, seqan::Tuple>, seqan::Tag>>, seqan::MergeStreamComparer, seqan::Tuple>, seqan::Tag>, seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 1>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:949:33: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 949 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: in instantiation of member function 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>::_freeHandlers' requested here 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1109:12: note: (skipping 12 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1109 | me.resize(new_length); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>>, seqan::PageBucket, seqan::Tuple>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less, seqan::Tuple>, seqan::Tag>, 1>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer, seqan::Tuple>, seqan::Tag>, seqan::SorterConfigSize, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:950:33: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 950 | if (writer) writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:114: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:98: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: warning: definition of implicit copy assignment operator for 'Triple, seqan::Tuple>, seqan::Tag>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 82 | inline Triple(Triple const &_p) | ^ /usr/include/c++/v1/__algorithm/sift_down.h:61:14: note: in implicit copy assignment operator for 'seqan::Triple, seqan::Tuple>, seqan::Tag>' first required here 61 | *__start = _Ops::__iter_move(__child_i); | ^ /usr/include/c++/v1/__algorithm/make_heap.h:39:12: note: in instantiation of function template specialization 'std::__sift_down, seqan::Tuple>, seqan::Tag>, 1>> &, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 39 | std::__sift_down<_AlgPolicy>(__first, __comp_ref, __n, __first + __start); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:41:8: note: in instantiation of function template specialization 'std::__make_heap, seqan::Tuple>, seqan::Tag>, 1>> &, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 41 | std::__make_heap<_AlgPolicy>(__first, __middle, __comp); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:65:12: note: in instantiation of function template specialization 'std::__partial_sort_impl, seqan::Tuple>, seqan::Tag>, 1>> &, seqan::Triple, seqan::Tuple>, seqan::Tag> *, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 65 | std::__partial_sort_impl<_AlgPolicy>(__first, __middle, __last, static_cast<__comp_ref_type<_Compare> >(__comp)); | ^ /usr/include/c++/v1/__algorithm/sort.h:992:10: note: in instantiation of function template specialization 'std::__partial_sort, seqan::Tuple>, seqan::Tag>, 1>>, seqan::Triple, seqan::Tuple>, seqan::Tag> *, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 992 | std::__partial_sort<_AlgPolicy>( | ^ /usr/include/c++/v1/__algorithm/sort.h:1003:8: note: (skipping 19 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1003 | std::__sort_impl<_ClassicAlgPolicy>(std::move(__first), std::move(__last), __comp); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function, seqan::Tuple>, seqan::Tag>>, seqan::PageBucket, seqan::Tuple>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer, seqan::Tuple>, seqan::Tag>, seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 2>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType, seqan::Tuple>, seqan::Tag>>, seqan::MergeStreamComparer, seqan::Tuple>, seqan::Tag>, seqan::_skew7ExtendComp, seqan::Tuple>, seqan::Tag>, 2>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:949:33: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 949 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: in instantiation of member function 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>::_freeHandlers' requested here 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1109:12: note: (skipping 12 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1109 | me.resize(new_length); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>>, seqan::PageBucket, seqan::Tuple>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less, seqan::Tuple>, seqan::Tag>, 2>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer, seqan::Tuple>, seqan::Tag>, seqan::SorterConfigSize, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:950:33: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 950 | if (writer) writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple>, seqan::Tag>, seqan::Triple, seqan::Tuple>, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:114: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:98: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: warning: definition of implicit copy assignment operator for 'Triple, seqan::Tuple>, seqan::Tag>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 82 | inline Triple(Triple const &_p) | ^ /usr/include/c++/v1/__algorithm/sift_down.h:61:14: note: in implicit copy assignment operator for 'seqan::Triple, seqan::Tuple>, seqan::Tag>' first required here 61 | *__start = _Ops::__iter_move(__child_i); | ^ /usr/include/c++/v1/__algorithm/make_heap.h:39:12: note: in instantiation of function template specialization 'std::__sift_down, seqan::Tuple>, seqan::Tag>, 2>> &, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 39 | std::__sift_down<_AlgPolicy>(__first, __comp_ref, __n, __first + __start); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:41:8: note: in instantiation of function template specialization 'std::__make_heap, seqan::Tuple>, seqan::Tag>, 2>> &, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 41 | std::__make_heap<_AlgPolicy>(__first, __middle, __comp); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:65:12: note: in instantiation of function template specialization 'std::__partial_sort_impl, seqan::Tuple>, seqan::Tag>, 2>> &, seqan::Triple, seqan::Tuple>, seqan::Tag> *, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 65 | std::__partial_sort_impl<_AlgPolicy>(__first, __middle, __last, static_cast<__comp_ref_type<_Compare> >(__comp)); | ^ /usr/include/c++/v1/__algorithm/sort.h:992:10: note: in instantiation of function template specialization 'std::__partial_sort, seqan::Tuple>, seqan::Tag>, 2>>, seqan::Triple, seqan::Tuple>, seqan::Tag> *, seqan::Triple, seqan::Tuple>, seqan::Tag> *>' requested here 992 | std::__partial_sort<_AlgPolicy>( | ^ /usr/include/c++/v1/__algorithm/sort.h:1003:8: note: (skipping 19 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1003 | std::__sort_impl<_ClassicAlgPolicy>(std::move(__first), std::move(__last), __comp); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: 'unary_function, seqan::Tuple>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:473:17: note: in instantiation of member class 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::MapperSpec, seqan::Tuple>, seqan::Tag>>, unsigned long>>>, seqan::MapperAsyncWriter>::insertBucket' requested here 473 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::MapperSpec, seqan::Tuple>, seqan::Tag>>, unsigned long>>>, seqan::MapperAsyncWriter>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:899:25: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::MapperSpec, seqan::Tuple>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::MapperMemAdapter>, seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::MapperSpec, seqan::Tuple>, seqan::Tag>>, unsigned long>>>, seqan::MapperAsyncWriter>>, seqan::Tag>::begin' requested here 899 | writer->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1243:23: note: in instantiation of member function 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::MapperSpec, seqan::Tuple>, seqan::Tag>>, unsigned long>>>::beginWrite' requested here 1243 | return me.beginWrite(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:103:13: note: in instantiation of function template specialization 'seqan::beginWrite, seqan::Tuple>, seqan::Tag>, seqan::MapperSpec, seqan::Tuple>, seqan::Tag>>, unsigned long>>>' requested here 103 | beginWrite(out124))) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:17: note: (skipping 10 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::Tuple>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:107: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: 'unary_function>, unsigned long>' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:246:41: note: in instantiation of template class 'seqan::_skew3NMapLinear>>' requested here 246 | nmap_linear_t map_linear(length(namer)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:13: note: in instantiation of function template specialization 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew3>::process>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>>' requested here 218 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: note: in instantiation of member function 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew3>::Pipe' requested here 376 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:13: note: in instantiation of function template specialization 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>::process>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>>' requested here 312 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: note: in instantiation of member function 'seqan::Pipe>, seqan::MapperSpec>>, unsigned long>>>, seqan::Filter>>>>, seqan::Skew7>::Pipe' requested here 367 | TRecurse recurse(filter); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:13: note: (skipping 7 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 294 | process(_textIn); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, unsigned long>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function>, seqan::Tag>>, seqan::PageBucket>, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer>, seqan::Tag>, seqan::_skew3NComp>, seqan::Tag>>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType>, seqan::Tag>>, seqan::MergeStreamComparer>, seqan::Tag>, seqan::_skew3NComp>, seqan::Tag>>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:920:33: note: in instantiation of member function 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 920 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:785:13: note: in instantiation of member function 'seqan::Pool>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>::endRead' requested here 785 | endRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:237:41: note: (skipping 12 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 237 | TSortTuples sorter; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tag>>, seqan::PageBucket>, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function>, seqan::Tag>, seqan::Pair>, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less>, seqan::Tag>>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer>, seqan::Tag>, seqan::SorterConfigSize>, seqan::Tag>>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:25: note: in instantiation of member function 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 904 | writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 786 | endWrite(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Tag>, seqan::Pair>, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: 'unary_function>>, void>' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:473:17: note: in instantiation of member class 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>::insertBucket' requested here 473 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:899:25: note: in instantiation of member function 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::Tag>, seqan::MapperMemAdapter>, seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>>, seqan::Tag>::begin' requested here 899 | writer->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1243:23: note: in instantiation of member function 'seqan::Pool>, seqan::MapperSpec>>, unsigned long>>>::beginWrite' requested here 1243 | return me.beginWrite(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:16: note: in instantiation of function template specialization 'seqan::beginWrite>, seqan::MapperSpec>>, unsigned long>>>' requested here 1369 | return beginWrite(dest) && append(dest, src) && endWrite(dest); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:16: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1376 | return assign(dest, src); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:135:14: note: in instantiation of function template specialization 'seqan::control>, seqan::Tag>, seqan::SorterSpec>, seqan::Tag>>, unsigned long>>>' requested here 135 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:547:16: note: (skipping 16 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 547 | return control(me, ControlBeginRead()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: 'unary_function>>, void>' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:473:17: note: in instantiation of member class 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>::insertBucket' requested here 473 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:899:25: note: in instantiation of member function 'seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::Tag>, seqan::MapperMemAdapter>, seqan::Handler>, seqan::MapperSpec>>, unsigned long>>>, seqan::MapperAsyncWriter>>, seqan::Tag>::begin' requested here 899 | writer->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1243:23: note: in instantiation of member function 'seqan::Pool>, seqan::MapperSpec>>, unsigned long>>>::beginWrite' requested here 1243 | return me.beginWrite(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:16: note: in instantiation of function template specialization 'seqan::beginWrite>, seqan::MapperSpec>>, unsigned long>>>' requested here 1369 | return beginWrite(dest) && append(dest, src) && endWrite(dest); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:16: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1376 | return assign(dest, src); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: 'binary_function, seqan::Tuple, seqan::Tag>>, seqan::PageBucket, seqan::Tuple, seqan::Tag>>, bool>' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:61:11: note: in instantiation of template class 'seqan::MergeStreamComparer, seqan::Tuple, seqan::Tag>, seqan::_skew3ExtendComp, seqan::Tuple, seqan::Tag>>>' requested here 61 | TLess less; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:196:21: note: in instantiation of template class 'seqan::PriorityType, seqan::Tuple, seqan::Tag>>, seqan::MergeStreamComparer, seqan::Tuple, seqan::Tag>, seqan::_skew3ExtendComp, seqan::Tuple, seqan::Tag>>>>' requested here 196 | TPrioQueue pqueue; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:37: note: in instantiation of template class 'seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>' requested here 633 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:949:33: note: in instantiation of member function 'seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 949 | if (reader) reader->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: in instantiation of member function 'seqan::Pool, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>::_freeHandlers' requested here 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1109:12: note: (skipping 14 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1109 | me.resize(new_length); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple, seqan::Tag>>, seqan::PageBucket, seqan::Tuple, seqan::Tag>>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: 'binary_function, seqan::Tuple, seqan::Tag>, seqan::Triple, seqan::Tuple, seqan::Tag>, bool>' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:428:56: note: in instantiation of template class 'seqan::AdaptorCompare2Less, seqan::Tuple, seqan::Tag>>>' requested here 428 | AdaptorCompare2Less cmp(me.pool.handlerArgs); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:454:20: note: in instantiation of function template specialization 'seqan::processBuffer, seqan::Tuple, seqan::Tag>, seqan::SorterConfigSize, seqan::Tuple, seqan::Tag>>, unsigned long>>' requested here 454 | _write(processBuffer(*chain.last, *this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:561:39: note: in instantiation of member function 'seqan::BufferHandler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>::end' requested here 561 | else handler2->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:773:21: note: in instantiation of member function 'seqan::BufferHandler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::end' requested here 773 | handler.end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:950:33: note: in instantiation of member function 'seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::BufferHandler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>, seqan::AdapterSpec>::end' requested here 950 | if (writer) writer->end(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:806:13: note: (skipping 15 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 806 | _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function, seqan::Tuple, seqan::Tag>, seqan::Triple, seqan::Tuple, seqan::Tag>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:114: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:98: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: warning: definition of implicit copy assignment operator for 'Triple, seqan::Tuple, seqan::Tag>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 82 | inline Triple(Triple const &_p) | ^ /usr/include/c++/v1/__algorithm/sift_down.h:61:14: note: in implicit copy assignment operator for 'seqan::Triple, seqan::Tuple, seqan::Tag>' first required here 61 | *__start = _Ops::__iter_move(__child_i); | ^ /usr/include/c++/v1/__algorithm/make_heap.h:39:12: note: in instantiation of function template specialization 'std::__sift_down, seqan::Tuple, seqan::Tag>>> &, seqan::Triple, seqan::Tuple, seqan::Tag> *>' requested here 39 | std::__sift_down<_AlgPolicy>(__first, __comp_ref, __n, __first + __start); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:41:8: note: in instantiation of function template specialization 'std::__make_heap, seqan::Tuple, seqan::Tag>>> &, seqan::Triple, seqan::Tuple, seqan::Tag> *>' requested here 41 | std::__make_heap<_AlgPolicy>(__first, __middle, __comp); | ^ /usr/include/c++/v1/__algorithm/partial_sort.h:65:12: note: in instantiation of function template specialization 'std::__partial_sort_impl, seqan::Tuple, seqan::Tag>>> &, seqan::Triple, seqan::Tuple, seqan::Tag> *, seqan::Triple, seqan::Tuple, seqan::Tag> *>' requested here 65 | std::__partial_sort_impl<_AlgPolicy>(__first, __middle, __last, static_cast<__comp_ref_type<_Compare> >(__comp)); | ^ /usr/include/c++/v1/__algorithm/sort.h:992:10: note: in instantiation of function template specialization 'std::__partial_sort, seqan::Tuple, seqan::Tag>>>, seqan::Triple, seqan::Tuple, seqan::Tag> *, seqan::Triple, seqan::Tuple, seqan::Tag> *>' requested here 992 | std::__partial_sort<_AlgPolicy>( | ^ /usr/include/c++/v1/__algorithm/sort.h:1003:8: note: (skipping 21 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 1003 | std::__sort_impl<_ClassicAlgPolicy>(std::move(__first), std::move(__last), __comp); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: 'unary_function, seqan::Tuple, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:473:17: note: in instantiation of member class 'seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::MapperSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::MapperAsyncWriter>::insertBucket' requested here 473 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::MapperSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::MapperAsyncWriter>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:899:25: note: in instantiation of member function 'seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::MapperSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::MapperMemAdapter>, seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::MapperSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::MapperAsyncWriter>>, seqan::Tag>::begin' requested here 899 | writer->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1243:23: note: in instantiation of member function 'seqan::Pool, seqan::Tuple, seqan::Tag>, seqan::MapperSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>::beginWrite' requested here 1243 | return me.beginWrite(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:74:13: note: in instantiation of function template specialization 'seqan::beginWrite, seqan::Tuple, seqan::Tag>, seqan::MapperSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>' requested here 74 | beginWrite(out12))) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:17: note: (skipping 12 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::Tuple, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function, seqan::Tuple, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:577:19: note: in instantiation of function template specialization 'seqan::control, seqan::Tuple, seqan::Tag>, seqan::SorterSpec, seqan::Tuple, seqan::Tag>>, unsigned long>>>' requested here 577 | return control(me.in1, command) && | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:150:14: note: (skipping 20 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 150 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::Tuple, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function, seqan::Tuple>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:594:19: note: in instantiation of function template specialization 'seqan::control, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 3>, unsigned long>>>' requested here 594 | return control(me.in1, command) && | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:490:14: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 490 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::Tuple>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function, seqan::Tuple>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:595:17: note: in instantiation of function template specialization 'seqan::control, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>' requested here 595 | control(me.in2, command) && | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:490:14: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 490 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::Tuple>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function, seqan::Tuple>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:596:17: note: in instantiation of function template specialization 'seqan::control, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 1>, unsigned long>>>' requested here 596 | control(me.in3, command) && | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:490:14: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 490 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::Tuple>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function, seqan::Tuple>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:597:17: note: in instantiation of function template specialization 'seqan::control, seqan::Tuple>, seqan::Tag>, seqan::SorterSpec, seqan::Tuple>, seqan::Tag>, 2>, unsigned long>>>' requested here 597 | control(me.in4, command) && | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:490:14: note: (skipping 13 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 490 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, seqan::Tuple>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:594:19: note: in instantiation of function template specialization 'seqan::control>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 3>, unsigned long>>>' requested here 594 | return control(me.in1, command) && | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:525:14: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 525 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:595:17: note: in instantiation of function template specialization 'seqan::control>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>' requested here 595 | control(me.in2, command) && | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:525:14: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 525 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<>>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:596:17: note: in instantiation of function template specialization 'seqan::control>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>, 1>, unsigned long>>>' requested here 596 | control(me.in3, command) && | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:525:14: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 525 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<>>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:42: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: 'unary_function>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>>, void>' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:226:17: note: in instantiation of member class 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>::insertBucket' requested here 226 | insertBucket(*this)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:603:46: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>::begin' requested here 603 | else return handler2->begin(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:916:25: note: in instantiation of member function 'seqan::Handler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>, seqan::AdapterSpec>, seqan::Handler>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>, seqan::Tag>>, seqan::Tag>::begin' requested here 916 | reader->begin()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1215:23: note: in instantiation of member function 'seqan::Pool>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>::beginRead' requested here 1215 | return me.beginRead(); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:597:17: note: in instantiation of function template specialization 'seqan::control>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, seqan::SorterSpec>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>, 2>, unsigned long>>>' requested here 597 | control(me.in4, command) && | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:525:14: note: (skipping 11 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) 525 | if (!control(me.in, command)) return false; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:5: note: in instantiation of function template specialization 'seqan::indexRequire>>, seqan::IndexSa<>, seqan::FibreSA_>' requested here 195 | indexRequire(index, FibreSA()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:13: note: in instantiation of function template specialization 'seqan::_indexRequireTopDownIteration>>, void>' requested here 211 | _indexRequireTopDownIteration(_index); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function>, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<>>, seqan::Tag>>, void>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:142: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: warning: definition of implicit copy assignment operator for 'VertexSA>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 134 | VertexSA(VertexSA const & other) : | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: note: in implicit copy assignment operator for 'seqan::VertexSA>' first required here 1731 | it._parentDesc = value(it); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:5: note: in instantiation of function template specialization 'seqan::_historyClear>>, seqan::IndexSa<>>, seqan::Preorder>' requested here 311 | _historyClear(it); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:13: note: in instantiation of function template specialization 'seqan::goRoot>>, void, seqan::TopDown<>>' requested here 212 | goRoot(*this); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:137: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_base.h:222:9: warning: definition of implicit copy assignment operator for 'VertexEsa' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy] 222 | VertexEsa(VertexEsa const &other): | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:112:8: note: in implicit copy assignment operator for 'seqan::VertexEsa' first required here 112 | struct VertexSA : public VertexEsa | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: note: in implicit copy assignment operator for 'seqan::VertexSA>' first required here 1731 | it._parentDesc = value(it); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:5: note: in instantiation of function template specialization 'seqan::_historyClear>>, seqan::IndexSa<>>, seqan::Preorder>' requested here 311 | _historyClear(it); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:13: note: in instantiation of function template specialization 'seqan::goRoot>>, void, seqan::TopDown<>>' requested here 212 | goRoot(*this); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:13: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>::Iter' requested here 349 | TBase(_index) {} | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: note: in instantiation of member function 'seqan::Iter>>, seqan::IndexSa<>>, seqan::VSTree>>>::Iter' requested here 4874 | TConstrainedIterator myConstrainedIterator(myIndex); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:91: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: 'binary_function>, seqan::Pair>, bool>' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1572:15: note: in instantiation of template class 'seqan::QGramLessOffset_>, const seqan::StringSet>>>' requested here 1572 | QGramLessOffset_::Type, TText const>(text, newQ - oldQ, oldQ)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4878:9: note: in instantiation of function template specialization 'seqan::_refineQGramIndexBucket> *>, seqan::StringSet>>, int, int>' requested here 4878 | _refineQGramIndexBucket( | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:32: note: in instantiation of function template specialization 'correctReads, FionaPoisson_>' requested here 5533 | numCorrected = correctReads(store, options, FionaPoisson()); | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function>, seqan::Pair>, bool>' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:118: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'unary_function, char>' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::QualityExtractor>' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:491:67: note: in instantiation of template class 'seqan::ModifiedString>, seqan::ModView>>>' requested here 491 | ModifiedString > quals(seq); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:433:5: note: in instantiation of function template specialization 'seqan::writeRecord>, seqan::StreamIterator>>, seqan::String, seqan::String>>' requested here 433 | writeRecord(file.iter, meta, seq, Tag(), context(file).options); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:471:9: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::String>, seqan::TagFastq_>' requested here 471 | writeRecord(file, meta, seq, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:479:5: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::Tag>, seqan::String, seqan::String>, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList>>>>>>' requested here 479 | writeRecord(file, meta, seq, file.format); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5061:9: note: in instantiation of function template specialization 'seqan::writeRecord, seqan::String>>' requested here 5061 | writeRecord(outFile, id, seq); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5611:15: note: in instantiation of function template specialization 'writeOutput>' requested here 5611 | int res = writeOutput(numCorrected, store, options); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function, char>' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -W -Wall -pedantic -fopenmp=libomp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -isystem /usr/local/include -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -c -o apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp 1. parser at end of file 2. Code generation 3. Running pass 'Function Pass Manager' on module '/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp'. 4. Running pass 'X86 DAG->DAG Instruction Selection' on function '@_ZN5seqan6cancelINS_4PairImmNS_3TagINS_5Pack_EEEEENS_4FileINS_5AsyncIvEEEENS_7DynamicEEEbRNS_6BufferIT_NS_9PageFrameIT0_T1_EEEERSE_' #0 0x00003b870c4b60b9 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.19+0x38b60b9) #1 0x00003b870c4b3f75 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.19+0x38b3f75) #2 0x00003b870c4643ab (/usr/lib/libprivatellvm.so.19+0x38643ab) #3 0x00003b87110502dc (/lib/libthr.so.3+0x1a2dc) #4 0x00003b871104f8eb (/lib/libthr.so.3+0x198eb) #5 0x00003b87028a32d3 ([vdso]+0x2d3) #6 0x00003b870ba293c7 llvm::TargetLowering::LowerCallTo(llvm::TargetLowering::CallLoweringInfo&) const (/usr/lib/libprivatellvm.so.19+0x2e293c7) #7 0x00003b870ba45b44 llvm::SelectionDAGBuilder::lowerInvokable(llvm::TargetLowering::CallLoweringInfo&, llvm::BasicBlock const*) (/usr/lib/libprivatellvm.so.19+0x2e45b44) #8 0x00003b870ba3026f llvm::SelectionDAGBuilder::LowerCallTo(llvm::CallBase const&, llvm::SDValue, bool, bool, llvm::BasicBlock const*, llvm::TargetLowering::PtrAuthInfo const*) (/usr/lib/libprivatellvm.so.19+0x2e3026f) #9 0x00003b870ba1d3c1 llvm::SelectionDAGBuilder::visitCall(llvm::CallInst const&) (/usr/lib/libprivatellvm.so.19+0x2e1d3c1) #10 0x00003b870ba1325b llvm::SelectionDAGBuilder::visit(llvm::Instruction const&) (/usr/lib/libprivatellvm.so.19+0x2e1325b) #11 0x00003b870ba63069 llvm::SelectionDAGISel::SelectBasicBlock(llvm::ilist_iterator_w_bits, false, true>, llvm::ilist_iterator_w_bits, false, true>, bool&) (/usr/lib/libprivatellvm.so.19+0x2e63069) #12 0x00003b870ba62398 llvm::SelectionDAGISel::SelectAllBasicBlocks(llvm::Function const&) (/usr/lib/libprivatellvm.so.19+0x2e62398) #13 0x00003b870ba60afc llvm::SelectionDAGISel::runOnMachineFunction(llvm::MachineFunction&) (/usr/lib/libprivatellvm.so.19+0x2e60afc) #14 0x00003b870ba5f581 llvm::SelectionDAGISelLegacy::runOnMachineFunction(llvm::MachineFunction&) (/usr/lib/libprivatellvm.so.19+0x2e5f581) #15 0x00003b870b69427d llvm::MachineFunctionPass::runOnFunction(llvm::Function&) (/usr/lib/libprivatellvm.so.19+0x2a9427d) #16 0x00003b870bea34c2 llvm::FPPassManager::runOnFunction(llvm::Function&) (/usr/lib/libprivatellvm.so.19+0x32a34c2) #17 0x00003b870bea9104 llvm::FPPassManager::runOnModule(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a9104) #18 0x00003b870bea3d13 llvm::legacy::PassManagerImpl::run(llvm::Module&) (/usr/lib/libprivatellvm.so.19+0x32a3d13) #19 0x00003b870626cce3 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr, std::__1::unique_ptr>, clang::BackendConsumer*) (/usr/lib/libprivateclang.so.19+0x226cce3) #20 0x00003b870660aef3 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/usr/lib/libprivateclang.so.19+0x260aef3) #21 0x00003b8706c8fd29 clang::ParseAST(clang::Sema&, bool, bool) (/usr/lib/libprivateclang.so.19+0x2c8fd29) #22 0x00003b8706b21189 clang::FrontendAction::Execute() (/usr/lib/libprivateclang.so.19+0x2b21189) #23 0x00003b8706a9e294 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/usr/lib/libprivateclang.so.19+0x2a9e294) #24 0x00003b8706ba779c clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/usr/lib/libprivateclang.so.19+0x2ba779c) #25 0x00003b7ee202689e (/usr/bin/c+++0xd89e) #26 0x00003b7ee2033d53 (/usr/bin/c+++0x1ad53) #27 0x00003b870677d83e (/usr/lib/libprivateclang.so.19+0x277d83e) #28 0x00003b870c464146 llvm::CrashRecoveryContext::RunSafely(llvm::function_ref) (/usr/lib/libprivatellvm.so.19+0x3864146) #29 0x00003b870677cfb8 clang::driver::CC1Command::Execute(llvm::ArrayRef>, std::__1::basic_string, std::__1::allocator>*, bool*) const (/usr/lib/libprivateclang.so.19+0x277cfb8) #30 0x00003b8706740af4 clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/usr/lib/libprivateclang.so.19+0x2740af4) #31 0x00003b8706740d8c clang::driver::Compilation::ExecuteJobs(clang::driver::JobList const&, llvm::SmallVectorImpl>&, bool) const (/usr/lib/libprivateclang.so.19+0x2740d8c) #32 0x00003b870675d750 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl>&) (/usr/lib/libprivateclang.so.19+0x275d750) #33 0x00003b7ee20334c8 (/usr/bin/c+++0x1a4c8) #34 0x00003b7ee2031a92 (/usr/bin/c+++0x18a92) #35 0x00003b87127c737f __libc_start1 (/lib/libc.so.7+0x9137f) c++: error: clang frontend command failed with exit code 139 (use -v to see invocation) FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/fiona-0eb0c2.cpp c++: note: diagnostic msg: /tmp/fiona-0eb0c2.sh c++: note: diagnostic msg: ******************** ninja: build stopped: subcommand failed. ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped making "build" in /usr/ports/biology/seqan-apps =>> Cleaning up wrkdir ===> Cleaning for seqan-apps-2.4.0_11 build of biology/seqan-apps | seqan-apps-2.4.0_11 ended at Sat Dec 6 02:55:05 EST 2025 build time: 00:02:08 !!! build failure encountered !!!