=>> Building biology/biolibc build started at Fri Dec 26 20:32:52 EST 2025 port directory: /usr/ports/biology/biolibc package name: biolibc-0.2.7 building for: FreeBSD 143amd64-deluxe-desktop-job-02 14.3-RELEASE-p2 FreeBSD 14.3-RELEASE-p2 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 500 Jun 26 2025 /usr/ports/biology/biolibc/Makefile Ports top last git commit: 3dd9e2202282 Ports top unclean checkout: yes Port dir last git commit: f680350d5ef9 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4 Host OSVERSION: 1403000 Jail OSVERSION: 1403000 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p2 UNAME_r=14.3-RELEASE-p2 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=3.4.4 MASTERMNT=/mnt/data/.m/143amd64-deluxe-desktop/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/mnt/data/.m/143amd64-deluxe-desktop/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=143amd64-deluxe-desktop SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/mnt/data/.m/143amd64-deluxe-desktop/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4 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/biolibc/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biolibc/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/biolibc/work/.cache HOME=/wrkdirs/usr/ports/biology/biolibc/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/biolibc/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/biolibc/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/biolibc/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biolibc/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/biolibc/work/.cache HOME=/wrkdirs/usr/ports/biology/biolibc/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/biolibc/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/biolibc/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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/biolibc" EXAMPLESDIR="share/examples/biolibc" DATADIR="share/biolibc" WWWDIR="www/biolibc" ETCDIR="etc/biolibc" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/biolibc DOCSDIR=/usr/local/share/doc/biolibc EXAMPLESDIR=/usr/local/share/examples/biolibc WWWDIR=/usr/local/www/biolibc ETCDIR=/usr/local/etc/biolibc --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # Work around some weirdness when fetching golang modules GO_TAGS+=netcgo .if ${.CURDIR:M*/www/chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/www/ungoogled-chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/lang/rust*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/lang/gcc*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/www/iridium*} MAKE_JOBS_NUMBER=16 .endif .if ${.CURDIR:M*/devel/electron*} MAKE_JOBS_NUMBER=20 .endif .if ${.CURDIR:M*/databases/mongodb*} MAKE_JOBS_NUMBER=12 .endif .if ${.CURDIR:M*/devel/llvm*} MAKE_JOBS_NUMBER=16 .endif # Speed things up a bit MAKE_JOBS_NUMBER?=8 #### #### #MAKE_JOBS_NUMBER?=4 # Alows us to build ports non-interactivly DISABLE_LICENSES=yes LICENSES_ACCEPTED+= DCC # Enable SNDIO on anything that supports it #OPTIONS_SET+=PULSEAUDIO OPTIONS_SET+=SNDIO # Yes we have MS Windows x11-fonts_webfonts_SET+=EXTRAFONTS CLEARTYPE # Desktop Specific Options sysutils_gksu_UNSET+=NAUTILUS x11-wm_compiz-fusion_UNSET+=EMERALD accessibility_redshift_SET+=GUI VIDMODE # These ports default to other audio servers, audio_espeak_UNSET+=PORTAUDIO www_qt5-webengine_UNSET+=ALSA www_qt6-webengine_UNSET+=ALSA audio_rhvoice_UNSET+=AO comms_morse_UNSET+=OSS audio_harp_UNSET+=OSS # Somehow these options are being set and result in ports being rebuilt needlessly becuase they are actually turned off audio_alsa-plugins_SET+=FFMPEG JACK PULSEAUDIO SAMPLERATE SPEEX #### Misc Poudriere #### .include "/etc/make.conf.ports_env" ---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=nobody UID=65534 GID=65534 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> biolibc-0.2.7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [143amd64-deluxe-desktop-job-02] Installing pkg-2.5.1... [143amd64-deluxe-desktop-job-02] Extracting pkg-2.5.1: .......... done ===> biolibc-0.2.7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of biolibc-0.2.7 =========================================================================== =================================================== ===== 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 biolibc-0.2.7 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by biolibc-0.2.7 for building => SHA256 Checksum OK for auerlab-biolibc-0.2.7_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Fetching all distfiles required by biolibc-0.2.7 for building ===> Extracting for biolibc-0.2.7 => SHA256 Checksum OK for auerlab-biolibc-0.2.7_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for biolibc-0.2.7 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> biolibc-0.2.7 depends on shared library: libxtend.so - not found ===> Installing existing package /packages/All/libxtend-0.2.1.10.pkg [143amd64-deluxe-desktop-job-02] Installing libxtend-0.2.1.10... [143amd64-deluxe-desktop-job-02] Extracting libxtend-0.2.1.10: .......... done ===> biolibc-0.2.7 depends on shared library: libxtend.so - found (/usr/local/lib/libxtend.so) ===> Returning to build of biolibc-0.2.7 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for biolibc-0.2.7 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for biolibc-0.2.7 (cd /wrkdirs/usr/ports/biology/biolibc/work/biolibc-0.2.7 && /usr/bin/make LOCALBASE=/usr/local depend) rm -f Makefile.depend for file in *.c; do cc -isystem ../local/include -isystem /usr/local/include -MM ${file} >> Makefile.depend; printf "\t\${CC} -c \${CFLAGS} ${file}\n\n" >> Makefile.depend; done --- align.o --- --- align-mutators.o --- --- bed.o --- --- bed-mutators.o --- --- chrom-name-cmp.o --- --- fasta.o --- --- fasta-mutators.o --- --- fastq.o --- --- align.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include align.c --- align-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include align-mutators.c --- bed-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include bed-mutators.c --- bed.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include bed.c --- chrom-name-cmp.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include chrom-name-cmp.c --- fasta.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include fasta.c --- fasta-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include fasta-mutators.c --- fastq.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include fastq.c --- fastq-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include fastq-mutators.c --- fastx.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include fastx.c --- fastx-mutators.o --- --- gff3.o --- --- fastx-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include fastx-mutators.c --- gff3.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include gff3.c --- gff3-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include gff3-mutators.c --- gff3-index.o --- --- gff3-index-mutators.o --- --- gff3-index.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include gff3-index.c --- gff3-index-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include gff3-index-mutators.c --- orf.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include orf.c --- overlap.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include overlap.c --- overlap-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include overlap-mutators.c --- pos-list.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include pos-list.c --- pos-list-mutators.o --- --- sam.o --- --- pos-list-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include pos-list-mutators.c --- sam.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include sam.c --- sam-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include sam-mutators.c --- sam-buff.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include sam-buff.c --- sam-buff-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include sam-buff-mutators.c --- vcf.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include vcf.c --- vcf-mutators.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include vcf-mutators.c --- libbiolibc.a --- --- libbiolibc.so.2.0 --- --- libbiolibc.a --- ar r libbiolibc.a align.o align-mutators.o bed.o bed-mutators.o chrom-name-cmp.o fasta.o fasta-mutators.o fastq.o fastq-mutators.o fastx.o fastx-mutators.o gff3.o gff3-mutators.o gff3-index.o gff3-index-mutators.o orf.o overlap.o overlap-mutators.o pos-list.o pos-list-mutators.o sam.o sam-mutators.o sam-buff.o sam-buff-mutators.o vcf.o vcf-mutators.o --- libbiolibc.so.2.0 --- cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include -Wl,-soname=libbiolibc.so.2 -o libbiolibc.so.2.0 align.o align-mutators.o bed.o bed-mutators.o chrom-name-cmp.o fasta.o fasta-mutators.o fastq.o fastq-mutators.o fastx.o fastx-mutators.o gff3.o gff3-mutators.o gff3-index.o gff3-index-mutators.o orf.o overlap.o overlap-mutators.o pos-list.o pos-list-mutators.o sam.o sam-mutators.o sam-buff.o sam-buff-mutators.o vcf.o vcf-mutators.o --- libbiolibc.a --- ar: warning: creating libbiolibc.a ranlib libbiolibc.a =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for biolibc-0.2.7 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/lib /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/include/biolibc /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/share/man/man3 install -m 0444 *.h /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/include/biolibc install -m 0444 Man/*.3 /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/share/man/man3 install -m 0444 libbiolibc.a /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/lib install -m 0555 libbiolibc.so.2.0 /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/lib ln -sf libbiolibc.so.2.0 /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/lib/libbiolibc.so.2 ln -sf libbiolibc.so.2.0 /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/lib/libbiolibc.so chmod 0655 /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/lib/libbiolibc.so.2.0 strip /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/lib/libbiolibc.so.2.0 chmod 0555 /wrkdirs/usr/ports/biology/biolibc/work/stage/usr/local/lib/libbiolibc.so.2.0 ====> 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=2025-12-27T01:32:52+0000' 'PKG_NOTE_ports_top_git_hash=3dd9e2202282' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=f680350d5ef9' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.4' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for biolibc-0.2.7 ===> Building biolibc-0.2.7 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for biolibc-0.2.7 build of biology/biolibc | biolibc-0.2.7 ended at Fri Dec 26 20:32:56 EST 2025 build time: 00:00:05