=>> Building biology/bifrost build started at Fri Feb 20 13:40:18 EST 2026 port directory: /usr/ports/biology/bifrost package name: bifrost-1.3.5_1 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 571 Jun 29 2025 /usr/ports/biology/bifrost/Makefile Ports top last git commit: eac71dbf758c Ports top unclean checkout: no Port dir last git commit: bba37490f132 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 07 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bifrost/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bifrost/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bifrost/work/.cache HOME=/wrkdirs/usr/ports/biology/bifrost/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bifrost/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bifrost/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bifrost/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bifrost/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bifrost/work/.cache HOME=/wrkdirs/usr/ports/biology/bifrost/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bifrost/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bifrost/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/bifrost/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unqualified-std-cast-call " 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=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bifrost" EXAMPLESDIR="share/examples/bifrost" DATADIR="share/bifrost" WWWDIR="www/bifrost" ETCDIR="etc/bifrost" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bifrost DOCSDIR=/usr/local/share/doc/bifrost EXAMPLESDIR=/usr/local/share/examples/bifrost WWWDIR=/usr/local/www/bifrost ETCDIR=/usr/local/etc/bifrost --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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bifrost-1.3.5_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> bifrost-1.3.5_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bifrost-1.3.5_1 =========================================================================== =================================================== ===== 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 bifrost-1.3.5_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bifrost-1.3.5_1 for building => SHA256 Checksum OK for pmelsted-bifrost-v1.3.5_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 bifrost-1.3.5_1 for building ===> Extracting for bifrost-1.3.5_1 => SHA256 Checksum OK for pmelsted-bifrost-v1.3.5_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 bifrost-1.3.5_1 ===> Applying FreeBSD patches for bifrost-1.3.5_1 from /usr/ports/biology/bifrost/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bifrost-1.3.5_1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.10_1.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.10_1... [pkg.DaveG.ca] `-- Installing expat-2.7.4... [pkg.DaveG.ca] `-- Extracting expat-2.7.4: .......... 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-1.52.0... [pkg.DaveG.ca] `-- Extracting libuv-1.52.0: .......... done [pkg.DaveG.ca] `-- Installing rhash-1.4.6... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] `-- Extracting rhash-1.4.6: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.10_1: .......... done ===> bifrost-1.3.5_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of bifrost-1.3.5_1 ===> bifrost-1.3.5_1 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.13.2,4.pkg [pkg.DaveG.ca] Installing ninja-1.13.2,4... [pkg.DaveG.ca] `-- Installing python311-3.11.14_2... [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-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14_2: .......... done [pkg.DaveG.ca] Extracting ninja-1.13.2,4: ..... done ===== Message from python311-3.11.14_2: -- 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 ===> bifrost-1.3.5_1 depends on executable: ninja - found ===> Returning to build of bifrost-1.3.5_1 ===> bifrost-1.3.5_1 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. ===> bifrost-1.3.5_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of bifrost-1.3.5_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for bifrost-1.3.5_1 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/bifrost/work/.build CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- 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 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE Disabling native architecture compilation (including AVX2) Build type: Release Maximum k-mer size: 31 Maximum g-mer size: 31 -- Found ZLIB: /usr/lib/libz.so (found version "1.3.1") -- Configuring done (3.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_MODULE_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /wrkdirs/usr/ports/biology/bifrost/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for bifrost-1.3.5_1 [ 3% 29/32] /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.3.5/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unqualified-std-cast-call -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing 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-Dbifrost_dynamic_EXPORTS -I/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.3.5/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unqualified-std-cast-call -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unqualified-std-cast-call -DNDEBUG -fPIC -MD -MT src/CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o -MF src/CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o.d -o src/CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o -c /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.3.5/src/Kmer.cpp [ 12% 29/32] /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.3.5/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unqualified-std-cast-call -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unqualified-std-cast-call -DNDEBUG -MD -MT src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o -MF src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o.d -o src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o -c 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-DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.3.5/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unqualified-std-cast-call -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unqualified-std-cast-call -DNDEBUG -MD -MT src/CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o -MF src/CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o.d -o src/CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o -c /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.3.5/src/TinyBitmap.cpp [ 28% 29/32] /usr/local/libexec/ccache/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.3.5/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unqualified-std-cast-call -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unqualified-std-cast-call -DNDEBUG -MD -MT src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o -MF src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o.d -o 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/wrkdirs/usr/ports/biology/bifrost/work/stage/usr/local/include/bifrost/rw_spin_lock.h -- Installing: /wrkdirs/usr/ports/biology/bifrost/work/stage/usr/local/include/bifrost/strict_fstream.hpp -- Installing: /wrkdirs/usr/ports/biology/bifrost/work/stage/usr/local/include/bifrost/wyhash.h -- Installing: /wrkdirs/usr/ports/biology/bifrost/work/stage/usr/local/include/bifrost/zstr.hpp ====> 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=2026-02-20T18:40:18+0000' 'PKG_NOTE_ports_top_git_hash=eac71dbf758c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=bba37490f132' '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 bifrost-1.3.5_1 ===> Building bifrost-1.3.5_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for bifrost-1.3.5_1 build of biology/bifrost | bifrost-1.3.5_1 ended at Fri Feb 20 13:41:25 EST 2026 build time: 00:01:12