=>> Building biology/pbbam build started at Wed Oct 1 02:40:16 EDT 2025 port directory: /usr/ports/biology/pbbam package name: pbbam-0.18.0_12 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1055 Jun 29 20:14 /usr/ports/biology/pbbam/Makefile Ports top last git commit: a936fb9b16ba Ports top unclean checkout: no Port dir last git commit: 18632db919ce Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500064 Jail OSVERSION: 1500064 Job Id: 06 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500064 UNAME_v=FreeBSD 15.0-ALPHA3 1500064 UNAME_r=15.0-ALPHA3 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_c_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_c_x64-HEAD-ALL/06/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_c_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_c_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--- ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix /usr/local --localstatedir /var --infodir share/info --auto-features=enabled -Dpython.bytecompile=-1 -Db_colorout=never --buildtype release --optimization plain --strip _build --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/pbbam/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pbbam/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/pbbam/work/.cache HOME=/wrkdirs/usr/ports/biology/pbbam/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/pbbam/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/pbbam/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/pbbam/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pbbam/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/pbbam/work/.cache HOME=/wrkdirs/usr/ports/biology/pbbam/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/pbbam/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/pbbam/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/pbbam/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/pbbam" EXAMPLESDIR="share/examples/pbbam" DATADIR="share/pbbam" WWWDIR="www/pbbam" ETCDIR="etc/pbbam" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pbbam DOCSDIR=/usr/local/share/doc/pbbam EXAMPLESDIR=/usr/local/share/examples/pbbam WWWDIR=/usr/local/www/pbbam ETCDIR=/usr/local/etc/pbbam --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 ===> NOTICE: The pbbam port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pbbam-0.18.0_12 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.3.1.pkg [pkg.DaveG.ca] Installing pkg-2.3.1... [pkg.DaveG.ca] Extracting pkg-2.3.1: .......... done ===> pbbam-0.18.0_12 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pbbam-0.18.0_12 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The pbbam port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by pbbam-0.18.0_12 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The pbbam port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by pbbam-0.18.0_12 for building => SHA256 Checksum OK for PacificBiosciences-pbbam-0.18.0_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 ===> NOTICE: The pbbam port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by pbbam-0.18.0_12 for building ===> Extracting for pbbam-0.18.0_12 => SHA256 Checksum OK for PacificBiosciences-pbbam-0.18.0_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 pbbam-0.18.0_12 ===> Applying FreeBSD patches for pbbam-0.18.0_12 from /usr/ports/biology/pbbam/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pbbam-0.18.0_12 depends on executable: meson - not found ===> Installing existing package /packages/All/meson-1.7.0.pkg [pkg.DaveG.ca] Installing meson-1.7.0... [pkg.DaveG.ca] `-- Installing ninja-1.13.1,4... [pkg.DaveG.ca] | `-- Installing python311-3.11.13_1... [pkg.DaveG.ca] | | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | `-- Extracting gettext-runtime-0.23.1: .......... done [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-8.2.13_2... [pkg.DaveG.ca] | | `-- Extracting readline-8.2.13_2: .......... done [pkg.DaveG.ca] | `-- Extracting python311-3.11.13_1: .......... done [pkg.DaveG.ca] `-- Extracting ninja-1.13.1,4: ..... done [pkg.DaveG.ca] Extracting meson-1.7.0: .......... done ===== Message from python311-3.11.13_1: -- 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 ===> pbbam-0.18.0_12 depends on executable: meson - found ===> Returning to build of pbbam-0.18.0_12 ===> pbbam-0.18.0_12 depends on executable: ninja - found ===> pbbam-0.18.0_12 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... done ===> pbbam-0.18.0_12 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of pbbam-0.18.0_12 ===> pbbam-0.18.0_12 depends on file: /usr/local/bin/python3.11 - found ===> pbbam-0.18.0_12 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. ===> pbbam-0.18.0_12 depends on file: /usr/local/bin/ccache - found ===> Returning to build of pbbam-0.18.0_12 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pbbam-0.18.0_12 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.22.pkg [pkg.DaveG.ca] Installing htslib-1.22... [pkg.DaveG.ca] `-- Installing curl-8.15.0... [pkg.DaveG.ca] | `-- Installing brotli-1.1.0,1... [pkg.DaveG.ca] | `-- Extracting brotli-1.1.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing libunistring-1.3... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.3: .......... done [pkg.DaveG.ca] | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | `-- Installing libnghttp2-1.67.0... [pkg.DaveG.ca] | `-- Extracting libnghttp2-1.67.0: ....... done [pkg.DaveG.ca] | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] | `-- Installing zstd-1.5.7... [pkg.DaveG.ca] | | `-- Installing liblz4-1.10.0,1... [pkg.DaveG.ca] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg.DaveG.ca] | `-- Extracting zstd-1.5.7: .......... done [pkg.DaveG.ca] `-- Extracting curl-8.15.0: .......... done [pkg.DaveG.ca] `-- Installing libdeflate-1.24... [pkg.DaveG.ca] `-- Extracting libdeflate-1.24: .......... done [pkg.DaveG.ca] Extracting htslib-1.22: .......... done ===> pbbam-0.18.0_12 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of pbbam-0.18.0_12 ===> pbbam-0.18.0_12 depends on shared library: libboost_regex.so - not found ===> Installing existing package /packages/All/boost-libs-1.88.0_2.pkg [pkg.DaveG.ca] Installing boost-libs-1.88.0_2... [pkg.DaveG.ca] `-- Installing icu-76.1,1... [pkg.DaveG.ca] `-- Extracting icu-76.1,1: .......... done [pkg.DaveG.ca] Extracting boost-libs-1.88.0_2: .......... done ===== Message from boost-libs-1.88.0_2: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> pbbam-0.18.0_12 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Returning to build of pbbam-0.18.0_12 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for pbbam-0.18.0_12 WARNING: Recommend using either -Dbuildtype or -Doptimization + -Ddebug. Using both is redundant since they override each other. See: https://mesonbuild.com/Builtin-options.html#build-type-options The Meson build system Version: 1.7.0 Source dir: /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0 Build dir: /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build Build type: native build Project name: PacBioBAM Project version: 0.18.0 C++ compiler for the host machine: c++ (clang 19.1.7 "FreeBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)") C++ linker for the host machine: c++ ld.lld 19.1.7 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wduplicated-cond: NO Compiler for C++ supports arguments -Wduplicated-branches: NO Compiler for C++ supports arguments -Wlogical-op: NO Compiler for C++ supports arguments -Wrestrict: NO Compiler for C++ supports arguments -Wnull-dereference: YES Compiler for C++ supports arguments -Wuseless-cast: NO Compiler for C++ supports arguments -Wdouble-promotion: YES Compiler for C++ supports arguments -Wshadow: YES Compiler for C++ supports arguments -Wformat=1: NO Run-time dependency threads found: YES Found pkg-config: YES (/usr/local/bin/pkgconf) 2.4.3 Run-time dependency Boost found: YES 1.88.0 (/usr/local) Run-time dependency zlib found: YES 1.3.1 Run-time dependency htslib found: YES 1.22 Program python3.11 found: YES (/usr/local/bin/python3.11) Configuring Bam2SamVersion.h using configuration Configuring PbIndexVersion.h using configuration Configuring PbIndexDumpVersion.h using configuration Configuring PbMergeVersion.h using configuration Configuring PbBamifyVersion.h using configuration Build targets in project: 6 NOTICE: Future-deprecated features used: * 0.56.0: {'dependency.get_pkgconfig_variable'} PacBioBAM 0.18.0 User defined options auto_features : enabled b_colorout : never buildtype : release infodir : share/info localstatedir : /var optimization : plain prefix : /usr/local python.bytecompile: -1 strip : true Found ninja-1.13.1 at /usr/local/bin/ninja WARNING: Running the setup command as `meson [options]` instead of `meson setup [options]` is ambiguous and deprecated. =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for pbbam-0.18.0_12 [ 0% 16/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/Accuracy.cpp.o -MF src/libpbbam.so.0.18.0.p/Accuracy.cpp.o.d -o src/libpbbam.so.0.18.0.p/Accuracy.cpp.o -c ../src/Accuracy.cpp [ 1% 17/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/CigarOperation.cpp.o -MF src/libpbbam.so.0.18.0.p/CigarOperation.cpp.o.d -o src/libpbbam.so.0.18.0.p/CigarOperation.cpp.o -c ../src/CigarOperation.cpp [ 2% 18/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/Config.cpp.o -MF src/libpbbam.so.0.18.0.p/Config.cpp.o.d -o src/libpbbam.so.0.18.0.p/Config.cpp.o -c ../src/Config.cpp [ 3% 19/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/Cigar.cpp.o -MF src/libpbbam.so.0.18.0.p/Cigar.cpp.o.d -o src/libpbbam.so.0.18.0.p/Cigar.cpp.o -c ../src/Cigar.cpp [ 4% 20/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/ChemistryTable.cpp.o -MF src/libpbbam.so.0.18.0.p/ChemistryTable.cpp.o.d -o src/libpbbam.so.0.18.0.p/ChemistryTable.cpp.o -c ../src/ChemistryTable.cpp [ 5% 21/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/BamFile.cpp.o -MF src/libpbbam.so.0.18.0.p/BamFile.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamFile.cpp.o -c ../src/BamFile.cpp [ 6% 22/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/BaiIndexedBamReader.cpp.o -MF src/libpbbam.so.0.18.0.p/BaiIndexedBamReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/BaiIndexedBamReader.cpp.o -c ../src/BaiIndexedBamReader.cpp [ 7% 23/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/AlignmentPrinter.cpp.o -MF src/libpbbam.so.0.18.0.p/AlignmentPrinter.cpp.o.d -o src/libpbbam.so.0.18.0.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp In file included from ../src/AlignmentPrinter.cpp:9: ../include/pbbam/AlignmentPrinter.h:44:5: warning: explicitly defaulted move constructor is implicitly deleted [-Wdefaulted-function-deleted] 44 | AlignmentPrinter(AlignmentPrinter&&) = default; | ^ ../include/pbbam/AlignmentPrinter.h:70:47: note: move constructor of 'AlignmentPrinter' is implicitly deleted because field 'ifr_' has a deleted move constructor 70 | const std::unique_ptr ifr_; | ^ /usr/include/c++/v1/__memory/unique_ptr.h:215:55: note: copy constructor is implicitly deleted because 'unique_ptr' has a user-declared move constructor 215 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 unique_ptr(unique_ptr&& __u) _NOEXCEPT | ^ ../include/pbbam/AlignmentPrinter.h:44:44: note: replace 'default' with 'delete' 44 | AlignmentPrinter(AlignmentPrinter&&) = default; | ^~~~~~~ | delete ../include/pbbam/AlignmentPrinter.h:46:23: warning: explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted] 46 | AlignmentPrinter& operator=(AlignmentPrinter&&) = default; | ^ ../include/pbbam/AlignmentPrinter.h:70:47: note: move assignment operator of 'AlignmentPrinter' is implicitly deleted because field 'ifr_' has no move assignment operator 70 | const std::unique_ptr ifr_; | ^ ../include/pbbam/AlignmentPrinter.h:46:55: note: replace 'default' with 'delete' 46 | AlignmentPrinter& operator=(AlignmentPrinter&&) = default; | ^~~~~~~ | delete 2 warnings generated. [ 8% 24/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/DataSetElement.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetElement.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetElement.cpp.o -c ../src/DataSetElement.cpp [ 9% 25/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/BamRecordBuilder.cpp.o -MF src/libpbbam.so.0.18.0.p/BamRecordBuilder.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamRecordBuilder.cpp.o -c ../src/BamRecordBuilder.cpp [ 10% 26/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/Compare.cpp.o -MF src/libpbbam.so.0.18.0.p/Compare.cpp.o.d -o src/libpbbam.so.0.18.0.p/Compare.cpp.o -c ../src/Compare.cpp [ 11% 27/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/DataSet.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSet.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSet.cpp.o -c ../src/DataSet.cpp [ 12% 28/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/BamWriter.cpp.o -MF src/libpbbam.so.0.18.0.p/BamWriter.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamWriter.cpp.o -c ../src/BamWriter.cpp [ 13% 29/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/DataSetBaseTypes.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetBaseTypes.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetBaseTypes.cpp.o -c ../src/DataSetBaseTypes.cpp [ 14% 30/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/BamRecordImpl.cpp.o -MF src/libpbbam.so.0.18.0.p/BamRecordImpl.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamRecordImpl.cpp.o -c ../src/BamRecordImpl.cpp ../src/BamRecordImpl.cpp:93:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 93 | bam_copy1(d_.get(), other.d_.get()); | ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ ../src/BamRecordImpl.cpp:233:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 233 | bam_copy1(result.d_.get(), rawData.get()); | ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. [ 15% 31/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/FileProducer.cpp.o -MF src/libpbbam.so.0.18.0.p/FileProducer.cpp.o.d -o src/libpbbam.so.0.18.0.p/FileProducer.cpp.o -c ../src/FileProducer.cpp [ 16% 32/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/FastaReader.cpp.o -MF src/libpbbam.so.0.18.0.p/FastaReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/FastaReader.cpp.o -c ../src/FastaReader.cpp [ 17% 33/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/BamReader.cpp.o -MF src/libpbbam.so.0.18.0.p/BamReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamReader.cpp.o -c ../src/BamReader.cpp [ 18% 34/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/BamHeader.cpp.o -MF src/libpbbam.so.0.18.0.p/BamHeader.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamHeader.cpp.o -c ../src/BamHeader.cpp [ 19% 35/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/DataSetXsd.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetXsd.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetXsd.cpp.o -c ../src/DataSetXsd.cpp [ 20% 36/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/BamRecordTags.cpp.o -MF src/libpbbam.so.0.18.0.p/BamRecordTags.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamRecordTags.cpp.o -c ../src/BamRecordTags.cpp [ 21% 37/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/FastqReader.cpp.o -MF src/libpbbam.so.0.18.0.p/FastqReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/FastqReader.cpp.o -c ../src/FastqReader.cpp [ 22% 38/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/BamTagCodec.cpp.o -MF src/libpbbam.so.0.18.0.p/BamTagCodec.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamTagCodec.cpp.o -c ../src/BamTagCodec.cpp [ 23% 39/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/MD5.cpp.o -MF src/libpbbam.so.0.18.0.p/MD5.cpp.o.d -o src/libpbbam.so.0.18.0.p/MD5.cpp.o -c ../src/MD5.cpp [ 24% 40/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/BamRecord.cpp.o -MF src/libpbbam.so.0.18.0.p/BamRecord.cpp.o.d -o src/libpbbam.so.0.18.0.p/BamRecord.cpp.o -c ../src/BamRecord.cpp [ 25% 41/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/FofnReader.cpp.o -MF src/libpbbam.so.0.18.0.p/FofnReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/FofnReader.cpp.o -c ../src/FofnReader.cpp [ 26% 42/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/Frames.cpp.o -MF src/libpbbam.so.0.18.0.p/Frames.cpp.o.d -o src/libpbbam.so.0.18.0.p/Frames.cpp.o -c ../src/Frames.cpp [ 27% 43/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/DataSetTypes.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp [ 28% 44/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/DataSetIO.cpp.o -MF src/libpbbam.so.0.18.0.p/DataSetIO.cpp.o.d -o src/libpbbam.so.0.18.0.p/DataSetIO.cpp.o -c ../src/DataSetIO.cpp [ 29% 45/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/BarcodeQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/BarcodeQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/BarcodeQuery.cpp.o -c ../src/BarcodeQuery.cpp In file included from ../src/BarcodeQuery.cpp:13: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : 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__)) | ^ 1 warning generated. [ 30% 46/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/IndexedFastaReader.cpp.o -MF src/libpbbam.so.0.18.0.p/IndexedFastaReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/IndexedFastaReader.cpp.o -c ../src/IndexedFastaReader.cpp [ 31% 47/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/FastaSequenceQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/FastaSequenceQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/FastaSequenceQuery.cpp.o -c ../src/FastaSequenceQuery.cpp [ 32% 48/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/FileUtils.cpp.o -MF src/libpbbam.so.0.18.0.p/FileUtils.cpp.o.d -o src/libpbbam.so.0.18.0.p/FileUtils.cpp.o -c ../src/FileUtils.cpp [ 33% 49/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/GenomicInterval.cpp.o -MF src/libpbbam.so.0.18.0.p/GenomicInterval.cpp.o.d -o src/libpbbam.so.0.18.0.p/GenomicInterval.cpp.o -c ../src/GenomicInterval.cpp [ 34% 50/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/MemoryUtils.cpp.o -MF src/libpbbam.so.0.18.0.p/MemoryUtils.cpp.o.d -o src/libpbbam.so.0.18.0.p/MemoryUtils.cpp.o -c ../src/MemoryUtils.cpp ../src/MemoryUtils.cpp:37:14: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] 37 | rawData->cigar_tab = nullptr; | ^ /usr/local/include/htslib/sam.h:84:29: note: 'cigar_tab' has been explicitly marked deprecated here 84 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | ^ /usr/local/include/htslib/hts_defs.h:96:49: note: expanded from macro 'HTS_DEPRECATED' 96 | #define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message))) | ^ 1 warning generated. [ 35% 51/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/EntireFileQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/EntireFileQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/EntireFileQuery.cpp.o -c ../src/EntireFileQuery.cpp In file included from ../src/EntireFileQuery.cpp:11: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : 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__)) | ^ 1 warning generated. [ 36% 52/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/QualityValue.cpp.o -MF src/libpbbam.so.0.18.0.p/QualityValue.cpp.o.d -o src/libpbbam.so.0.18.0.p/QualityValue.cpp.o -c ../src/QualityValue.cpp [ 37% 53/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/PbiFile.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFile.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFile.cpp.o -c ../src/PbiFile.cpp [ 38% 54/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/IndexedBamWriter.cpp.o -MF src/libpbbam.so.0.18.0.p/IndexedBamWriter.cpp.o.d -o src/libpbbam.so.0.18.0.p/IndexedBamWriter.cpp.o -c ../src/IndexedBamWriter.cpp [ 39% 55/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/GenomicIntervalQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/GenomicIntervalQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/GenomicIntervalQuery.cpp.o -c ../src/GenomicIntervalQuery.cpp In file included from ../src/GenomicIntervalQuery.cpp:11: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : 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__)) | ^ 1 warning generated. [ 40% 56/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/PbiFilterQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFilterQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFilterQuery.cpp.o -c ../src/PbiFilterQuery.cpp In file included from ../src/PbiFilterQuery.cpp:13: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : 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__)) | ^ 1 warning generated. [ 41% 57/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/PbiBuilder.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiBuilder.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiBuilder.cpp.o -c ../src/PbiBuilder.cpp ../src/PbiBuilder.cpp:640:17: warning: variable 'i' set but not used [-Wunused-but-set-variable] 640 | for (size_t i = 0; totalNumRead < currentRow_; ++i) { | ^ 1 warning generated. [ 42% 58/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/PbiIndexedBamReader.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiIndexedBamReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiIndexedBamReader.cpp.o -c ../src/PbiIndexedBamReader.cpp [ 43% 59/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/ProgramInfo.cpp.o -MF src/libpbbam.so.0.18.0.p/ProgramInfo.cpp.o.d -o src/libpbbam.so.0.18.0.p/ProgramInfo.cpp.o -c ../src/ProgramInfo.cpp [ 44% 60/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/PbiFilterTypes.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFilterTypes.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFilterTypes.cpp.o -c ../src/PbiFilterTypes.cpp [ 45% 61/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/PbiFilter.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiFilter.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiFilter.cpp.o -c ../src/PbiFilter.cpp [ 46% 62/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/ValidationException.cpp.o -MF src/libpbbam.so.0.18.0.p/ValidationException.cpp.o.d -o src/libpbbam.so.0.18.0.p/ValidationException.cpp.o -c ../src/ValidationException.cpp [ 47% 63/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/PbiIndexIO.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiIndexIO.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiIndexIO.cpp.o -c ../src/PbiIndexIO.cpp [ 48% 64/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/PbiRawData.cpp.o -MF src/libpbbam.so.0.18.0.p/PbiRawData.cpp.o.d -o src/libpbbam.so.0.18.0.p/PbiRawData.cpp.o -c ../src/PbiRawData.cpp [ 49% 65/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/VirtualRegionTypeMap.cpp.o -MF src/libpbbam.so.0.18.0.p/VirtualRegionTypeMap.cpp.o.d -o src/libpbbam.so.0.18.0.p/VirtualRegionTypeMap.cpp.o -c ../src/VirtualRegionTypeMap.cpp [ 50% 66/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/ReadGroupInfo.cpp.o -MF src/libpbbam.so.0.18.0.p/ReadGroupInfo.cpp.o.d -o src/libpbbam.so.0.18.0.p/ReadGroupInfo.cpp.o -c ../src/ReadGroupInfo.cpp [ 50% 67/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/QNameQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/QNameQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/QNameQuery.cpp.o -c ../src/QNameQuery.cpp In file included from ../src/QNameQuery.cpp:15: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : 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__)) | ^ 1 warning generated. [ 51% 68/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/SamWriter.cpp.o -MF src/libpbbam.so.0.18.0.p/SamWriter.cpp.o.d -o src/libpbbam.so.0.18.0.p/SamWriter.cpp.o -c ../src/SamWriter.cpp [ 52% 69/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/ReadAccuracyQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/ReadAccuracyQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/ReadAccuracyQuery.cpp.o -c ../src/ReadAccuracyQuery.cpp In file included from ../src/ReadAccuracyQuery.cpp:11: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : 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__)) | ^ 1 warning generated. [ 53% 70/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/SequenceInfo.cpp.o -MF src/libpbbam.so.0.18.0.p/SequenceInfo.cpp.o.d -o src/libpbbam.so.0.18.0.p/SequenceInfo.cpp.o -c ../src/SequenceInfo.cpp [ 54% 71/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/XmlWriter.cpp.o -MF src/libpbbam.so.0.18.0.p/XmlWriter.cpp.o.d -o src/libpbbam.so.0.18.0.p/XmlWriter.cpp.o -c ../src/XmlWriter.cpp ../src/XmlWriter.cpp:129:21: warning: loop variable 'prefixIter' creates a copy from type 'const value_type' (aka 'const pair') [-Wrange-loop-construct] 129 | for (const auto prefixIter : xsdPrefixesUsed) { | ^ ../src/XmlWriter.cpp:129:10: note: use reference type 'const value_type &' (aka 'const pair &') to prevent copying 129 | for (const auto prefixIter : xsdPrefixesUsed) { | ^~~~~~~~~~~~~~~~~~~~~~~ | & 1 warning generated. [ 55% 72/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/SamTagCodec.cpp.o -MF src/libpbbam.so.0.18.0.p/SamTagCodec.cpp.o.d -o src/libpbbam.so.0.18.0.p/SamTagCodec.cpp.o -c ../src/SamTagCodec.cpp [ 56% 73/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/Version.cpp.o -MF src/libpbbam.so.0.18.0.p/Version.cpp.o.d -o src/libpbbam.so.0.18.0.p/Version.cpp.o -c ../src/Version.cpp [ 57% 74/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/ValidationErrors.cpp.o -MF src/libpbbam.so.0.18.0.p/ValidationErrors.cpp.o.d -o src/libpbbam.so.0.18.0.p/ValidationErrors.cpp.o -c ../src/ValidationErrors.cpp [ 58% 75/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/Validator.cpp.o -MF src/libpbbam.so.0.18.0.p/Validator.cpp.o.d -o src/libpbbam.so.0.18.0.p/Validator.cpp.o -c ../src/Validator.cpp [ 59% 76/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/SubreadLengthQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/SubreadLengthQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/SubreadLengthQuery.cpp.o -c ../src/SubreadLengthQuery.cpp In file included from ../src/SubreadLengthQuery.cpp:13: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : 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__)) | ^ 1 warning generated. [ 60% 77/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/ZmwTypeMap.cpp.o -MF src/libpbbam.so.0.18.0.p/ZmwTypeMap.cpp.o.d -o src/libpbbam.so.0.18.0.p/ZmwTypeMap.cpp.o -c ../src/ZmwTypeMap.cpp [ 61% 78/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfVariant.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfVariant.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfVariant.cpp.o -c ../src/vcf/VcfVariant.cpp [ 62% 79/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/VirtualZmwReader.cpp.o -MF src/libpbbam.so.0.18.0.p/VirtualZmwReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/VirtualZmwReader.cpp.o -c ../src/VirtualZmwReader.cpp [ 63% 80/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfWriter.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfWriter.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfWriter.cpp.o -c ../src/vcf/VcfWriter.cpp [ 64% 81/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/VirtualZmwBamRecord.cpp.o -MF src/libpbbam.so.0.18.0.p/VirtualZmwBamRecord.cpp.o.d -o src/libpbbam.so.0.18.0.p/VirtualZmwBamRecord.cpp.o -c ../src/VirtualZmwBamRecord.cpp [ 65% 82/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/XmlReader.cpp.o -MF src/libpbbam.so.0.18.0.p/XmlReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/XmlReader.cpp.o -c ../src/XmlReader.cpp [ 66% 83/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/VirtualZmwCompositeReader.cpp.o -MF src/libpbbam.so.0.18.0.p/VirtualZmwCompositeReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/VirtualZmwCompositeReader.cpp.o -c ../src/VirtualZmwCompositeReader.cpp [ 67% 84/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfReader.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfReader.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfReader.cpp.o -c ../src/vcf/VcfReader.cpp [ 68% 85/102] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2Sam.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2Sam.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2Sam.cpp.o -c ../tools/bam2sam/src/Bam2Sam.cpp [ 69% 86/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfHeader.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfHeader.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfHeader.cpp.o -c ../src/vcf/VcfHeader.cpp [ 70% 87/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfFormat.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfFormat.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfFormat.cpp.o -c ../src/vcf/VcfFormat.cpp ../src/vcf/VcfFormat.cpp:481:29: warning: loop variable 'fieldValue' creates a copy from type 'const std::string' [-Wrange-loop-construct] 481 | for (const auto fieldValue : fieldValues) { | ^ ../src/vcf/VcfFormat.cpp:481:18: note: use reference type 'const std::string &' to prevent copying 481 | for (const auto fieldValue : fieldValues) { | ^~~~~~~~~~~~~~~~~~~~~~~ | & ../src/vcf/VcfFormat.cpp:521:21: warning: loop variable 'field' creates a copy from type 'const PacBio::VCF::InfoField' [-Wrange-loop-construct] 521 | for (const auto field : fields) { | ^ ../src/vcf/VcfFormat.cpp:521:10: note: use reference type 'const PacBio::VCF::InfoField &' to prevent copying 521 | for (const auto field : fields) { | ^~~~~~~~~~~~~~~~~~ | & ../src/vcf/VcfFormat.cpp:541:25: warning: loop variable 'id' creates a copy from type 'const std::string' [-Wrange-loop-construct] 541 | for (const auto id : genotypeIds) { | ^ ../src/vcf/VcfFormat.cpp:541:14: note: use reference type 'const std::string &' to prevent copying 541 | for (const auto id : genotypeIds) { | ^~~~~~~~~~~~~~~ | & ../src/vcf/VcfFormat.cpp:548:25: warning: loop variable 'sampleGenotype' creates a copy from type 'const PacBio::VCF::GenotypeField' [-Wrange-loop-construct] 548 | for (const auto sampleGenotype : sampleGenotypes) { | ^ ../src/vcf/VcfFormat.cpp:548:14: note: use reference type 'const PacBio::VCF::GenotypeField &' to prevent copying 548 | for (const auto sampleGenotype : sampleGenotypes) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | & 4 warnings generated. [ 71% 88/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/ZmwReadStitcher.cpp.o -MF src/libpbbam.so.0.18.0.p/ZmwReadStitcher.cpp.o.d -o src/libpbbam.so.0.18.0.p/ZmwReadStitcher.cpp.o -c ../src/ZmwReadStitcher.cpp [ 72% 89/102] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbindex.p/pbindex_src_PbIndex.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndex.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndex.cpp.o -c ../tools/pbindex/src/PbIndex.cpp [ 73% 90/102] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/bam2sam.p/bam2sam_src_main.cpp.o -MF tools/bam2sam.p/bam2sam_src_main.cpp.o.d -o tools/bam2sam.p/bam2sam_src_main.cpp.o -c ../tools/bam2sam/src/main.cpp ../tools/bam2sam/src/main.cpp:72:25: warning: loop variable 'e' creates a copy from type 'const std::string' [-Wrange-loop-construct] 72 | for (const auto e : settings.errors_) | ^ ../tools/bam2sam/src/main.cpp:72:14: note: use reference type 'const std::string &' to prevent copying 72 | for (const auto e : settings.errors_) | ^~~~~~~~~~~~~~ | & 1 warning generated. [ 74% 91/102] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbindex.p/pbindex_src_main.cpp.o -MF tools/pbindex.p/pbindex_src_main.cpp.o.d -o tools/pbindex.p/pbindex_src_main.cpp.o -c ../tools/pbindex/src/main.cpp ../tools/pbindex/src/main.cpp:57:25: warning: loop variable 'e' creates a copy from type 'const std::string' [-Wrange-loop-construct] 57 | for (const auto e : settings.errors_) | ^ ../tools/pbindex/src/main.cpp:57:14: note: use reference type 'const std::string &' to prevent copying 57 | for (const auto e : settings.errors_) | ^~~~~~~~~~~~~~ | & 1 warning generated. [ 75% 92/102] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbindex.p/common_OptionParser.cpp.o -MF tools/pbindex.p/common_OptionParser.cpp.o.d -o tools/pbindex.p/common_OptionParser.cpp.o -c ../tools/common/OptionParser.cpp [ 76% 93/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o -c ../tools/pbindexdump/src/CppFormatter.cpp [ 77% 94/102] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/bam2sam.p/common_OptionParser.cpp.o -MF tools/bam2sam.p/common_OptionParser.cpp.o.d -o tools/bam2sam.p/common_OptionParser.cpp.o -c ../tools/common/OptionParser.cpp [ 78% 95/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/pugixml_pugixml.cpp.o -MF src/libpbbam.so.0.18.0.p/pugixml_pugixml.cpp.o.d -o src/libpbbam.so.0.18.0.p/pugixml_pugixml.cpp.o -c ../src/pugixml/pugixml.cpp [ 79% 96/102] c++ -o tools/bam2sam tools/bam2sam.p/common_OptionParser.cpp.o tools/bam2sam.p/bam2sam_src_main.cpp.o tools/bam2sam.p/bam2sam_src_Bam2Sam.cpp.o -Wl,--as-needed -Wl,--no-undefined -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -Wl,--start-group /usr/local/lib/libhts.so -pthread /usr/lib/libz.so -Wl,--end-group [ 80% 96/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/WhitelistedZmwReadStitcher.cpp.o -MF src/libpbbam.so.0.18.0.p/WhitelistedZmwReadStitcher.cpp.o.d -o src/libpbbam.so.0.18.0.p/WhitelistedZmwReadStitcher.cpp.o -c ../src/WhitelistedZmwReadStitcher.cpp [ 81% 96/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfQuery.cpp.o -c ../src/vcf/VcfQuery.cpp In file included from ../src/vcf/VcfQuery.cpp:1: ../include/pbbam/vcf/VcfQuery.h:23:5: warning: explicitly defaulted default constructor is implicitly deleted [-Wdefaulted-function-deleted] 23 | VcfQuery() = default; | ^ ../include/pbbam/vcf/VcfQuery.h:39:15: note: default constructor of 'VcfQuery' is implicitly deleted because field 'reader_' has a deleted default constructor 39 | VcfReader reader_; | ^ ../include/pbbam/vcf/VcfReader.h:26:5: note: 'VcfReader' has been explicitly marked deleted here 26 | VcfReader() = delete; | ^ ../include/pbbam/vcf/VcfQuery.h:23:18: note: replace 'default' with 'delete' 23 | VcfQuery() = default; | ^~~~~~~ | delete 1 warning generated. [ 82% 96/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbindexdump.p/pbindexdump_src_PbIndexDump.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDump.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDump.cpp.o -c ../tools/pbindexdump/src/PbIndexDump.cpp [ 83% 96/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbindexdump.p/common_OptionParser.cpp.o -MF tools/pbindexdump.p/common_OptionParser.cpp.o.d -o tools/pbindexdump.p/common_OptionParser.cpp.o -c ../tools/common/OptionParser.cpp [ 84% 96/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/ZmwGroupQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/ZmwGroupQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/ZmwGroupQuery.cpp.o -c ../src/ZmwGroupQuery.cpp In file included from ../src/ZmwGroupQuery.cpp:17: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : 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__)) | ^ 1 warning generated. [ 85% 96/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/ZmwQuery.cpp.o -MF src/libpbbam.so.0.18.0.p/ZmwQuery.cpp.o.d -o src/libpbbam.so.0.18.0.p/ZmwQuery.cpp.o -c ../src/ZmwQuery.cpp In file included from ../src/ZmwQuery.cpp:13: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : 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__)) | ^ 1 warning generated. [ 86% 96/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -c ../tools/pbindexdump/src/JsonFormatter.cpp [ 87% 96/102] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbmerge.p/common_OptionParser.cpp.o -MF tools/pbmerge.p/common_OptionParser.cpp.o.d -o tools/pbmerge.p/common_OptionParser.cpp.o -c ../tools/common/OptionParser.cpp [ 88% 96/102] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbbamify.p/common_OptionParser.cpp.o -MF tools/pbbamify.p/common_OptionParser.cpp.o.d -o tools/pbbamify.p/common_OptionParser.cpp.o -c ../tools/common/OptionParser.cpp [ 89% 96/102] c++ -Isrc/libpbbam.so.0.18.0.p -Isrc -I../src -Iinclude -I../include -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DBOOST_ALL_NO_LIB -pthread -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ src/libpbbam.so.0.18.0.p/vcf_VcfSort.cpp.o -MF src/libpbbam.so.0.18.0.p/vcf_VcfSort.cpp.o.d -o src/libpbbam.so.0.18.0.p/vcf_VcfSort.cpp.o -c ../src/vcf/VcfSort.cpp In file included from ../src/vcf/VcfSort.cpp:11: ../include/pbbam/vcf/VcfQuery.h:23:5: warning: explicitly defaulted default constructor is implicitly deleted [-Wdefaulted-function-deleted] 23 | VcfQuery() = default; | ^ ../include/pbbam/vcf/VcfQuery.h:39:15: note: default constructor of 'VcfQuery' is implicitly deleted because field 'reader_' has a deleted default constructor 39 | VcfReader reader_; | ^ ../include/pbbam/vcf/VcfReader.h:26:5: note: 'VcfReader' has been explicitly marked deleted here 26 | VcfReader() = delete; | ^ ../include/pbbam/vcf/VcfQuery.h:23:18: note: replace 'default' with 'delete' 23 | VcfQuery() = default; | ^~~~~~~ | delete 1 warning generated. [ 90% 97/102] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbindexdump.p/pbindexdump_src_main.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_main.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -c ../tools/pbindexdump/src/main.cpp ../tools/pbindexdump/src/main.cpp:93:25: warning: loop variable 'e' creates a copy from type 'const std::string' [-Wrange-loop-construct] 93 | for (const auto e : settings.errors_) | ^ ../tools/pbindexdump/src/main.cpp:93:14: note: use reference type 'const std::string &' to prevent copying 93 | for (const auto e : settings.errors_) | ^~~~~~~~~~~~~~ | & 1 warning generated. [ 91% 97/102] c++ -o src/libpbbam.so.0.18.0 src/libpbbam.so.0.18.0.p/Accuracy.cpp.o src/libpbbam.so.0.18.0.p/AlignmentPrinter.cpp.o src/libpbbam.so.0.18.0.p/BaiIndexedBamReader.cpp.o src/libpbbam.so.0.18.0.p/BamFile.cpp.o src/libpbbam.so.0.18.0.p/BamHeader.cpp.o src/libpbbam.so.0.18.0.p/BamReader.cpp.o src/libpbbam.so.0.18.0.p/BamRecord.cpp.o src/libpbbam.so.0.18.0.p/BamRecordBuilder.cpp.o src/libpbbam.so.0.18.0.p/BamRecordImpl.cpp.o src/libpbbam.so.0.18.0.p/BamRecordTags.cpp.o src/libpbbam.so.0.18.0.p/BamTagCodec.cpp.o src/libpbbam.so.0.18.0.p/BamWriter.cpp.o src/libpbbam.so.0.18.0.p/BarcodeQuery.cpp.o src/libpbbam.so.0.18.0.p/ChemistryTable.cpp.o src/libpbbam.so.0.18.0.p/Cigar.cpp.o src/libpbbam.so.0.18.0.p/CigarOperation.cpp.o src/libpbbam.so.0.18.0.p/Compare.cpp.o src/libpbbam.so.0.18.0.p/Config.cpp.o src/libpbbam.so.0.18.0.p/DataSet.cpp.o src/libpbbam.so.0.18.0.p/DataSetBaseTypes.cpp.o src/libpbbam.so.0.18.0.p/DataSetElement.cpp.o src/libpbbam.so.0.18.0.p/DataSetIO.cpp.o src/libpbbam.so.0.18.0.p/DataSetTypes.cpp.o src/libpbbam.so.0.18.0.p/DataSetXsd.cpp.o src/libpbbam.so.0.18.0.p/EntireFileQuery.cpp.o src/libpbbam.so.0.18.0.p/FastaReader.cpp.o src/libpbbam.so.0.18.0.p/FastaSequenceQuery.cpp.o src/libpbbam.so.0.18.0.p/FastqReader.cpp.o src/libpbbam.so.0.18.0.p/FileProducer.cpp.o src/libpbbam.so.0.18.0.p/FileUtils.cpp.o src/libpbbam.so.0.18.0.p/FofnReader.cpp.o src/libpbbam.so.0.18.0.p/Frames.cpp.o src/libpbbam.so.0.18.0.p/GenomicInterval.cpp.o src/libpbbam.so.0.18.0.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.0.18.0.p/IndexedBamWriter.cpp.o src/libpbbam.so.0.18.0.p/IndexedFastaReader.cpp.o src/libpbbam.so.0.18.0.p/MD5.cpp.o src/libpbbam.so.0.18.0.p/MemoryUtils.cpp.o src/libpbbam.so.0.18.0.p/PbiBuilder.cpp.o src/libpbbam.so.0.18.0.p/PbiFile.cpp.o src/libpbbam.so.0.18.0.p/PbiFilter.cpp.o src/libpbbam.so.0.18.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.0.18.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.0.18.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.0.18.0.p/PbiIndexIO.cpp.o src/libpbbam.so.0.18.0.p/PbiRawData.cpp.o src/libpbbam.so.0.18.0.p/ProgramInfo.cpp.o src/libpbbam.so.0.18.0.p/QNameQuery.cpp.o src/libpbbam.so.0.18.0.p/QualityValue.cpp.o src/libpbbam.so.0.18.0.p/ReadAccuracyQuery.cpp.o src/libpbbam.so.0.18.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.0.18.0.p/SamTagCodec.cpp.o src/libpbbam.so.0.18.0.p/SamWriter.cpp.o src/libpbbam.so.0.18.0.p/SequenceInfo.cpp.o src/libpbbam.so.0.18.0.p/SubreadLengthQuery.cpp.o src/libpbbam.so.0.18.0.p/Validator.cpp.o src/libpbbam.so.0.18.0.p/ValidationErrors.cpp.o src/libpbbam.so.0.18.0.p/ValidationException.cpp.o src/libpbbam.so.0.18.0.p/Version.cpp.o src/libpbbam.so.0.18.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.0.18.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.0.18.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.0.18.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.0.18.0.p/XmlReader.cpp.o src/libpbbam.so.0.18.0.p/XmlWriter.cpp.o src/libpbbam.so.0.18.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.0.18.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.0.18.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.0.18.0.p/ZmwQuery.cpp.o src/libpbbam.so.0.18.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfQuery.cpp.o src/libpbbam.so.0.18.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.0.18.0.p/pugixml_pugixml.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,-soname,libpbbam.so.0.18.0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -pthread -Wl,--start-group /usr/lib/libz.so /usr/local/lib/libhts.so -Wl,--end-group [ 92% 98/102] /usr/local/bin/meson --internal symbolextractor /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build src/libpbbam.so.0.18.0 src/libpbbam.so.0.18.0 src/libpbbam.so.0.18.0.p/libpbbam.so.0.18.0.symbols [ 93% 100/102] c++ -o tools/pbindex tools/pbindex.p/common_OptionParser.cpp.o tools/pbindex.p/pbindex_src_main.cpp.o tools/pbindex.p/pbindex_src_PbIndex.cpp.o -Wl,--as-needed -Wl,--no-undefined -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include '-Wl,-rpath,$ORIGIN/../src:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build/src -Wl,-rpath-link,/usr/local/lib -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group [ 94% 100/102] c++ -o tools/pbindexdump tools/pbindexdump.p/common_OptionParser.cpp.o tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDump.cpp.o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include '-Wl,-rpath,$ORIGIN/../src:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build/src -Wl,-rpath-link,/usr/local/lib -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group [ 95% 100/102] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbbamify.p/pbbamify_src_main.cpp.o -MF tools/pbbamify.p/pbbamify_src_main.cpp.o.d -o tools/pbbamify.p/pbbamify_src_main.cpp.o -c ../tools/pbbamify/src/main.cpp [ 96% 100/102] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -MF tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o.d -o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -c ../tools/pbbamify/src/QueryLookup.cpp [ 97% 100/102] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbmerge.p/pbmerge_src_main.cpp.o -MF tools/pbmerge.p/pbmerge_src_main.cpp.o.d -o tools/pbmerge.p/pbmerge_src_main.cpp.o -c ../tools/pbmerge/src/main.cpp In file included from ../tools/pbmerge/src/main.cpp:9: In file included from ../tools/pbmerge/../common/BamFileMerger.h:40: In file included from ../tools/pbmerge/../common/BamFileMerger.inl:9: In file included from ../include/pbbam/CompositeBamReader.h:226: ../include/pbbam/internal/CompositeBamReader.inl:171:30: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 171 | struct PositionSorter : 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 ../tools/pbmerge/src/main.cpp:9: In file included from ../tools/pbmerge/../common/BamFileMerger.h:40: ../tools/pbmerge/../common/BamFileMerger.inl:75:27: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 75 | struct QNameSorter : std::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__)) | ^ ../tools/pbmerge/src/main.cpp:95:25: warning: loop variable 'e' creates a copy from type 'const std::string' [-Wrange-loop-construct] 95 | for (const auto e : settings.errors_) | ^ ../tools/pbmerge/src/main.cpp:95:14: note: use reference type 'const std::string &' to prevent copying 95 | for (const auto e : settings.errors_) | ^~~~~~~~~~~~~~ | & 3 warnings generated. [ 98% 101/102] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -I/usr/local/include -fdiagnostics-color=never -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -DBOOST_ALL_NO_LIB -Wnull-dereference -Wdouble-promotion -Wshadow -MD -MQ tools/pbbamify.p/pbbamify_src_PbBamify.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamify.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamify.cpp.o -c ../tools/pbbamify/src/PbBamify.cpp [ 99% 102/102] c++ -o tools/pbmerge tools/pbmerge.p/common_OptionParser.cpp.o tools/pbmerge.p/pbmerge_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include '-Wl,-rpath,$ORIGIN/../src:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build/src -Wl,-rpath-link,/usr/local/lib -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group [100% 102/102] c++ -o tools/pbbamify tools/pbbamify.p/common_OptionParser.cpp.o tools/pbbamify.p/pbbamify_src_main.cpp.o tools/pbbamify.p/pbbamify_src_PbBamify.cpp.o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -Wl,--as-needed -Wl,--no-undefined -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include '-Wl,-rpath,$ORIGIN/../src:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build/src -Wl,-rpath-link,/usr/local/lib -Wl,--start-group src/libpbbam.so.0.18.0 /usr/local/lib/libhts.so /usr/lib/libz.so -Wl,--end-group =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pbbam-0.18.0_12 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for pbbam-0.18.0_12 ===> Generating temporary packing list [ 0% 1/1] /usr/local/bin/meson install --no-rebuild Installing src/libpbbam.so.0.18.0 to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib Stripping target 'src/libpbbam.so.0.18.0'. Installing tools/bam2sam to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/bin Stripping target 'tools/bam2sam'. Installing tools/pbindex to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/bin Stripping target 'tools/pbindex'. Installing tools/pbindexdump to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/bin Stripping target 'tools/pbindexdump'. Installing tools/pbmerge to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/bin Stripping target 'tools/pbmerge'. Installing tools/pbbamify to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/bin Stripping target 'tools/pbbamify'. Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Accuracy.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/AlignmentPrinter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BaiIndexedBamReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamFile.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamHeader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamRecord.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamRecordBuilder.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamRecordImpl.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamRecordTag.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamRecordView.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamTagCodec.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BamWriter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/BarcodeQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Cigar.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/CigarOperation.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ClipType.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Compare.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/CompositeBamReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/CompositeFastaReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Config.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/DataSet.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/DataSetTypes.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/DataSetXsd.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/EntireFileQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FastaReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FastaSequence.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FastaSequenceQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FastqReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FastqSequence.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/FrameEncodingType.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Frames.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/GenomicInterval.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/GenomicIntervalQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/IndexedBamWriter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/IndexedFastaReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Interval.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/IRecordWriter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/LocalContextFlags.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/MakeUnique.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/MD5.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/MoveAppend.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Orientation.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiBasicTypes.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiBuilder.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiFile.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiFilter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiFilterQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiFilterTypes.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiIndexedBamReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PbiRawData.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Position.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ProgramInfo.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PulseBehavior.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/PulseExclusionReason.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/QNameQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/QualityValue.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/QualityValues.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ReadAccuracyQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ReadGroupInfo.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/RecordType.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/SamTagCodec.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/SamWriter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/SequenceInfo.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Strand.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/StringUtilities.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/SubreadLengthQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Tag.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/TagCollection.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Unused.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/Validator.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ZmwGroupQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ZmwQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ZmwType.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/ZmwTypeMap.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/exception/BundleChemistryMappingException.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/exception Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/exception/InvalidSequencingChemistryException.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/exception Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/exception/ValidationException.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/exception Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Accuracy.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/BamHeader.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/BamRecord.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/BamRecordBuilder.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/BamRecordImpl.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/BamRecordView.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Cigar.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/CigarOperation.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Compare.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/CompositeBamReader.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/CompositeFastaReader.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSet.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetBaseTypes.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetBaseTypes.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetElement.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetElement.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetListElement.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetListElement.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/DataSetTypes.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/FastaSequence.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/FastqSequence.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Frames.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/GenomicInterval.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Interval.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/PbiBasicTypes.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/PbiFilter.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/PbiFilterTypes.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/PbiRawData.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/ProgramInfo.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/QualityValue.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/QualityValues.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/QueryBase.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/QueryBase.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/ReadGroupInfo.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/SequenceInfo.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Tag.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/internal/Validator.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfVariant.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfFile.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfFormat.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfHeader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfHeaderTypes.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfSort.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfQuery.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/VcfWriter.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/internal/VcfVariant.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/internal/VcfFile.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/internal/VcfHeader.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/vcf/internal/VcfHeaderTypes.inl to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/vcf/internal Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualPolymeraseBamRecord.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualPolymeraseReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualRegion.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualRegionType.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualRegionTypeMap.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/VirtualZmwBamRecord.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/WhitelistedZmwReadStitcher.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/ZmwReadStitcher.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/include/pbbam/virtual/ZmwWhitelistVirtualReader.h to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/include/pbbam/virtual Installing /wrkdirs/usr/ports/biology/pbbam/work/pbbam-0.18.0/_build/meson-private/pbbam.pc to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/libdata/pkgconfig Installing symlink pointing to libpbbam.so.0.18.0 to /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib/libpbbam.so install -l rs /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib/libpbbam.so.0.18.0 /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib/libpbbam.so.0.18 install -l rs /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib/libpbbam.so.0.18.0 /wrkdirs/usr/ports/biology/pbbam/work/stage/usr/local/lib/libpbbam.so.0 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-10-01T06:40:16+0000' 'PKG_NOTE_ports_top_git_hash=a936fb9b16ba' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=18632db919ce' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for pbbam-0.18.0_12 ===> Building pbbam-0.18.0_12 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for pbbam-0.18.0_12 build of biology/pbbam | pbbam-0.18.0_12 ended at Wed Oct 1 02:44:26 EDT 2025 build time: 00:04:17