=>> Building biology/biolibc build started at Thu May 1 19:09:45 BST 2025 port directory: /usr/ports/biology/biolibc package name: biolibc-0.2.7 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 500 Apr 30 08:35 /usr/ports/biology/biolibc/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: f680350d5e Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 04 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE 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/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/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/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=" -fstack-protector-strong " 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=14.2 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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 ===> biolibc-0.2.7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... 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 => auerlab-biolibc-0.2.7_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/auerlab/biolibc/tar.gz/0.2.7?dummy=/auerlab-biolibc-0.2.7_GH0.tar.gz fetch: https://codeload.github.com/auerlab/biolibc/tar.gz/0.2.7?dummy=/auerlab-biolibc-0.2.7_GH0.tar.gz: size unknown fetch: https://codeload.github.com/auerlab/biolibc/tar.gz/0.2.7?dummy=/auerlab-biolibc-0.2.7_GH0.tar.gz: size of remote file is not known auerlab-biolibc-0.2.7_GH0.tar.gz 146 kB 6014 kBps 00s ===> 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=root UID=0 GID=0 ===> 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=root UID=0 GID=0 ===> Patching for biolibc-0.2.7 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> biolibc-0.2.7 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] 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. ===> biolibc-0.2.7 depends on file: /usr/local/bin/ccache - found ===> Returning to build of biolibc-0.2.7 =========================================================================== =================================================== ===== 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.pkg [pkg-builder.dan.net.uk] Installing libxtend-0.2.1... [pkg-builder.dan.net.uk] Extracting libxtend-0.2.1: .......... 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=root UID=0 GID=0 ===> Configuring for biolibc-0.2.7 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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 cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include align.c 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 cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include bed.c 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 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 cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include fasta.c 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 cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include fastq.c 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 cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include fastx.c 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 cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include gff3.c 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 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 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 cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include orf.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include overlap.c 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 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 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 cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include sam.c 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 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 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 cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-char-subscripts -fPIC -isystem /usr/local/include -isystem /usr/local/include vcf.c 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 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 ar: warning: creating libbiolibc.a ranlib libbiolibc.a 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 -fstack-protector-strong =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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=2025-05-01T18:09:45+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=f680350d5e' '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 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 Thu May 1 19:09:51 BST 2025 build time: 00:00:06