=>> Building biology/mashmap build started at Thu Dec 11 22:34:23 EST 2025 port directory: /usr/ports/biology/mashmap package name: mashmap-3.1.3 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 858 Aug 27 2024 /usr/ports/biology/mashmap/Makefile Ports top last git commit: 62d8b1999233 Ports top unclean checkout: no Port dir last git commit: f98bd5d62996 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 02 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 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_13_5_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_13_5_x64-HEAD-ALL/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for mashmap-3.1.3: NATIVE=off: Use native optimization (-march=native) ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mashmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mashmap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mashmap/work/.cache HOME=/wrkdirs/usr/ports/biology/mashmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mashmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mashmap/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/mashmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mashmap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mashmap/work/.cache HOME=/wrkdirs/usr/ports/biology/mashmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mashmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mashmap/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/mashmap/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=" -L/usr/local/lib " LIBS="" 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-- CMAKE_BUILD_TYPE="release" OSREL=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/mashmap" EXAMPLESDIR="share/examples/mashmap" DATADIR="share/mashmap" WWWDIR="www/mashmap" ETCDIR="etc/mashmap" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mashmap DOCSDIR=/usr/local/share/doc/mashmap EXAMPLESDIR=/usr/local/share/examples/mashmap WWWDIR=/usr/local/www/mashmap ETCDIR=/usr/local/etc/mashmap --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 --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mashmap-3.1.3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> mashmap-3.1.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mashmap-3.1.3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mashmap-3.1.3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mashmap-3.1.3 for building => SHA256 Checksum OK for marbl-MashMap-v3.1.3_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mashmap-3.1.3 for building ===> Extracting for mashmap-3.1.3 => SHA256 Checksum OK for marbl-MashMap-v3.1.3_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 mashmap-3.1.3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mashmap-3.1.3 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.9.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.9... [pkg.DaveG.ca] `-- Installing expat-2.7.3... [pkg.DaveG.ca] `-- Extracting expat-2.7.3: .......... done [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Installing libunistring-1.4.1... [pkg.DaveG.ca] | `-- Extracting libunistring-1.4.1: .......... done [pkg.DaveG.ca] `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] `-- Installing libuv-1.51.0... [pkg.DaveG.ca] `-- Extracting libuv-1.51.0: .......... done [pkg.DaveG.ca] `-- Installing rhash-1.4.4_2... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] `-- Extracting rhash-1.4.4_2: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.9: .......... done ===> mashmap-3.1.3 depends on file: /usr/local/bin/cmake - found ===> Returning to build of mashmap-3.1.3 ===> mashmap-3.1.3 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.13.1,4.pkg [pkg.DaveG.ca] Installing ninja-1.13.1,4... [pkg.DaveG.ca] `-- Installing python311-3.11.14... [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.1... [pkg.DaveG.ca] | `-- Extracting readline-8.3.1: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] Extracting ninja-1.13.1,4: ..... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> mashmap-3.1.3 depends on executable: ninja - found ===> Returning to build of mashmap-3.1.3 ===> mashmap-3.1.3 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 ===> mashmap-3.1.3 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of mashmap-3.1.3 ===> mashmap-3.1.3 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. ===> mashmap-3.1.3 depends on file: /usr/local/bin/ccache - found ===> Returning to build of mashmap-3.1.3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mashmap-3.1.3 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.1_1.pkg [pkg.DaveG.ca] Installing gsl-2.7.1_1... [pkg.DaveG.ca] Extracting gsl-2.7.1_1: .......... done ===> mashmap-3.1.3 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of mashmap-3.1.3 ===> mashmap-3.1.3 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-8.17.0... [pkg.DaveG.ca] | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | `-- Extracting libnghttp2-1.68.0: ....... 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_1... [pkg.DaveG.ca] | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] `-- Extracting curl-8.17.0: .......... done [pkg.DaveG.ca] `-- Installing libdeflate-1.25... [pkg.DaveG.ca] `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] Extracting htslib-1.22: .......... done ===> mashmap-3.1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of mashmap-3.1.3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for mashmap-3.1.3 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/mashmap/work/.build -- The C compiler identification is Clang 19.1.7 -- The CXX compiler identification is Clang 19.1.7 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_BUILD_TYPE: Release -- Found PkgConfig: /usr/local/bin/pkgconf (found version "2.4.3") -- Checking for module 'htslib' -- Found htslib, version 1.22 -- Configuring done (10.7s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/mashmap/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for mashmap-3.1.3 [ 16% 4/6] /usr/local/libexec/ccache/c++ -DUSE_HTSLIB -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o -MF CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o.d -o CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/utils.cpp [ 33% 4/6] /usr/local/libexec/ccache/c++ -DUSE_HTSLIB -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap.dir/src/common/utils.cpp.o -MF CMakeFiles/mashmap.dir/src/common/utils.cpp.o.d -o CMakeFiles/mashmap.dir/src/common/utils.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/utils.cpp [ 50% 4/6] /usr/local/libexec/ccache/c++ -DUSE_HTSLIB -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -MF CMakeFiles/mashmap-align.dir/src/align/align.cpp.o.d -o CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/align/align.cpp In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/align/align.cpp:18: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/align/include/parseCmdArgs.hpp:16: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/parseCmdArgs.hpp:16: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/map_parameters.hpp:14: /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:560:40: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 560 | uint32_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:560:40: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:592:40: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 592 | uint64_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:592:40: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:624:41: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 624 | uint128_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:624:41: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1019:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1019 | char temp[length + 1]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1019:15: note: read of non-const variable 'length' is not allowed in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1017:9: note: declared here 1017 | int length = l[seed_no]; | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1054:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1054 | char temp[length - 1]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1054:15: note: read of non-const variable 'length' is not allowed in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1051:9: note: declared here 1051 | int length = l[seed_no]; | ^ In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/align/align.cpp:18: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/align/include/parseCmdArgs.hpp:16: /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/parseCmdArgs.hpp:601:24: warning: implicit conversion from 'type' (aka 'unsigned long') to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] 601 | = frac * std::numeric_limits::max(); | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 6 warnings generated. [ 66% 5/6] : && /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/mashmap-align.dir/link.d CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -o bin/mashmap-align -lgsl -lgslcblas -lm -lpthread -lz /usr/local/lib/libhts.so && : [ 83% 5/6] /usr/local/libexec/ccache/c++ -DUSE_HTSLIB -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -MF CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o.d -o CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/mash_map.cpp In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/mash_map.cpp:13: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/map_parameters.hpp:14: /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:560:40: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 560 | uint32_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:560:40: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:592:40: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 592 | uint64_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:592:40: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:624:41: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 624 | uint128_t one_seed = 0, all_seeds[NO_SEEDS], one_region = 0; | ^~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:624:41: note: function parameter 'NO_SEEDS' with unknown value cannot be used in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:555:49: note: declared here 555 | double ESTIMATE_SENSITIVITY(char** SEEDS, int NO_SEEDS, long long N) | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1019:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1019 | char temp[length + 1]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1019:15: note: read of non-const variable 'length' is not allowed in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1017:9: note: declared here 1017 | int length = l[seed_no]; | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1054:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1054 | char temp[length - 1]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1054:15: note: read of non-const variable 'length' is not allowed in a constant expression /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/ALeS.hpp:1051:9: note: declared here 1051 | int length = l[seed_no]; | ^ In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/mash_map.cpp:15: /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/parseCmdArgs.hpp:601:24: warning: implicit conversion from 'type' (aka 'unsigned long') to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] 601 | = frac * std::numeric_limits::max(); | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/mash_map.cpp:17: In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/map/include/computeMap.hpp:39: /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/robin-hood-hashing/robin_hood.h:1445:33: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 1445 | Cloner()(o, *this); | ^ /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.3/src/common/robin-hood-hashing/robin_hood.h:210:51: note: expanded from macro 'ROBIN_HOOD_IS_TRIVIALLY_COPYABLE' 210 | # define ROBIN_HOOD_IS_TRIVIALLY_COPYABLE(...) __has_trivial_copy(__VA_ARGS__) | ^ 7 warnings generated. [100% 6/6] : && /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -L/usr/local/lib -Xlinker --dependency-file=CMakeFiles/mashmap.dir/link.d CMakeFiles/mashmap.dir/src/common/utils.cpp.o CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -o bin/mashmap -lgsl -lgslcblas -lm -lpthread -lz /usr/local/lib/libhts.so && : =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for mashmap-3.1.3 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/biology/mashmap/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/mashmap/work/stage/usr/local/bin/mashmap -- Installing: /wrkdirs/usr/ports/biology/mashmap/work/stage/usr/local/bin/mashmap-align ====> 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=2025-12-12T03:34:23+0000' 'PKG_NOTE_ports_top_git_hash=62d8b1999233' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=f98bd5d62996' '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 mashmap-3.1.3 ===> Building mashmap-3.1.3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for mashmap-3.1.3 build of biology/mashmap | mashmap-3.1.3 ended at Thu Dec 11 22:36:14 EST 2025 build time: 00:01:58