=>> Building biology/fasda build started at Thu Feb 19 06:49:10 EST 2026 port directory: /usr/ports/biology/fasda package name: fasda-0.2.0.1 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 538 Jun 29 2025 /usr/ports/biology/fasda/Makefile Ports top last git commit: eac71dbf758c Ports top unclean checkout: no Port dir last git commit: 7611c373bf8f Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 01 ---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/01/.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/fasda/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fasda/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fasda/work/.cache HOME=/wrkdirs/usr/ports/biology/fasda/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fasda/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fasda/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fasda/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fasda/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fasda/work/.cache HOME=/wrkdirs/usr/ports/biology/fasda/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fasda/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fasda/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 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-- OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/fasda" EXAMPLESDIR="share/examples/fasda" DATADIR="share/fasda" WWWDIR="www/fasda" ETCDIR="etc/fasda" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fasda DOCSDIR=/usr/local/share/doc/fasda EXAMPLESDIR=/usr/local/share/examples/fasda WWWDIR=/usr/local/www/fasda ETCDIR=/usr/local/etc/fasda --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 ===> fasda-0.2.0.1 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 ===> fasda-0.2.0.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fasda-0.2.0.1 =========================================================================== =================================================== ===== 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 fasda-0.2.0.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by fasda-0.2.0.1 for building => SHA256 Checksum OK for auerlab-fasda-0.2.0-1-ga7d14ad_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 fasda-0.2.0.1 for building ===> Extracting for fasda-0.2.0.1 => SHA256 Checksum OK for auerlab-fasda-0.2.0-1-ga7d14ad_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 fasda-0.2.0.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fasda-0.2.0.1 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. ===> fasda-0.2.0.1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of fasda-0.2.0.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fasda-0.2.0.1 depends on shared library: libxtend.so - not found ===> Installing existing package /packages/All/libxtend-0.2.1.10.pkg [pkg.DaveG.ca] Installing libxtend-0.2.1.10... [pkg.DaveG.ca] Extracting libxtend-0.2.1.10: .......... done ===> fasda-0.2.0.1 depends on shared library: libxtend.so - found (/usr/local/lib/libxtend.so) ===> Returning to build of fasda-0.2.0.1 ===> fasda-0.2.0.1 depends on shared library: libbiolibc.so - not found ===> Installing existing package /packages/All/biolibc-0.2.7.pkg [pkg.DaveG.ca] Installing biolibc-0.2.7... [pkg.DaveG.ca] Extracting biolibc-0.2.7: .......... done ===> fasda-0.2.0.1 depends on shared library: libbiolibc.so - found (/usr/local/lib/libbiolibc.so) ===> Returning to build of fasda-0.2.0.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for fasda-0.2.0.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for fasda-0.2.0.1 --- fasda.o --- --- alignment-stats-mutators.o --- --- abundance.o --- --- normalize.o --- --- fold-change.o --- --- mann-whitney.o --- --- exact-p-val.o --- --- pval-sim.o --- --- fc-ge.o --- --- fasda.o --- cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include fasda.c --- alignment-stats-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include alignment-stats-mutators.c --- abundance.o --- cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include abundance.c --- fold-change.o --- cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include fold-change.c --- normalize.o --- cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include normalize.c --- mann-whitney.o --- cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include mann-whitney.c --- fc-ge.o --- cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include fc-ge.c --- exact-p-val.o --- cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include exact-p-val.c --- pval-sim.o --- cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include pval-sim.c --- fasda --- cc -o fasda fasda.o alignment-stats-mutators.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lbiolibc -lxtend -lm --- normalize --- cc -o normalize normalize.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lbiolibc -lxtend -lm --- abundance --- cc -o abundance abundance.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lbiolibc -lxtend -lm --- fold-change --- --- pval-sim --- cc -o pval-sim pval-sim.o fc-ge.o mann-whitney.o exact-p-val.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lbiolibc -lxtend -lm --- fold-change --- cc -o fold-change fold-change.o mann-whitney.o exact-p-val.o fc-ge.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lbiolibc -lxtend -lm =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fasda-0.2.0.1 depends on package: stringtie>0 - not found ===> Installing existing package /packages/All/stringtie-2.1.1.pkg [pkg.DaveG.ca] Installing stringtie-2.1.1... [pkg.DaveG.ca] Extracting stringtie-2.1.1: . done ===> fasda-0.2.0.1 depends on package: stringtie>0 - found ===> Returning to build of fasda-0.2.0.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for fasda-0.2.0.1 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/fasda/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/fasda/work/stage/usr/local/libexec/fasda /wrkdirs/usr/ports/biology/fasda/work/stage/usr/local/share/man/man1 install -m 0755 fasda /wrkdirs/usr/ports/biology/fasda/work/stage/usr/local/bin install -m 0755 abundance normalize fold-change pval-sim Scripts/* /wrkdirs/usr/ports/biology/fasda/work/stage/usr/local/libexec/fasda install -m 0644 Man/*.1 /wrkdirs/usr/ports/biology/fasda/work/stage/usr/local/share/man/man1 strip /wrkdirs/usr/ports/biology/fasda/work/stage/usr/local/bin/fasda for f in abundance normalize fold-change pval-sim; do strip /wrkdirs/usr/ports/biology/fasda/work/stage/usr/local/libexec/fasda/${f}; done ====> 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=2026-02-19T11:49:10+0000' 'PKG_NOTE_ports_top_git_hash=eac71dbf758c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=7611c373bf8f' '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 fasda-0.2.0.1 ===> Building fasda-0.2.0.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for fasda-0.2.0.1 build of biology/fasda | fasda-0.2.0.1 ended at Thu Feb 19 06:49:14 EST 2026 build time: 00:00:06