=>> Building biology/vcf2hap build started at Sat May 3 05:20:04 BST 2025 port directory: /usr/ports/biology/vcf2hap package name: vcf2hap-0.1.6.7_1 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 640 Dec 29 14:16 /usr/ports/biology/vcf2hap/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 01 ---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/01/.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/vcf2hap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcf2hap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcf2hap/work/.cache HOME=/wrkdirs/usr/ports/biology/vcf2hap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcf2hap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcf2hap/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-- VERSION=0.1.6.7 MANPREFIX=/usr/local/share XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcf2hap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcf2hap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcf2hap/work/.cache HOME=/wrkdirs/usr/ports/biology/vcf2hap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcf2hap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcf2hap/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/vcf2hap" EXAMPLESDIR="share/examples/vcf2hap" DATADIR="share/vcf2hap" WWWDIR="www/vcf2hap" ETCDIR="etc/vcf2hap" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vcf2hap DOCSDIR=/usr/local/share/doc/vcf2hap EXAMPLESDIR=/usr/local/share/examples/vcf2hap WWWDIR=/usr/local/www/vcf2hap ETCDIR=/usr/local/etc/vcf2hap --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 ===> vcf2hap-0.1.6.7_1 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 ===> vcf2hap-0.1.6.7_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vcf2hap-0.1.6.7_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 vcf2hap-0.1.6.7_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by vcf2hap-0.1.6.7_1 for building => SHA256 Checksum OK for auerlab-vcf2hap-0.1.6-7-gfda1765_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 vcf2hap-0.1.6.7_1 for building ===> Extracting for vcf2hap-0.1.6.7_1 => SHA256 Checksum OK for auerlab-vcf2hap-0.1.6-7-gfda1765_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 vcf2hap-0.1.6.7_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcf2hap-0.1.6.7_1 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. ===> vcf2hap-0.1.6.7_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of vcf2hap-0.1.6.7_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vcf2hap-0.1.6.7_1 depends on shared library: libbiolibc.so - not found ===> Installing existing package /packages/All/biolibc-0.2.7.pkg [pkg-builder.dan.net.uk] Installing biolibc-0.2.7... [pkg-builder.dan.net.uk] `-- Installing libxtend-0.2.1... [pkg-builder.dan.net.uk] `-- Extracting libxtend-0.2.1: .......... done [pkg-builder.dan.net.uk] Extracting biolibc-0.2.7: .......... done ===> vcf2hap-0.1.6.7_1 depends on shared library: libbiolibc.so - found (/usr/local/lib/libbiolibc.so) ===> Returning to build of vcf2hap-0.1.6.7_1 ===> vcf2hap-0.1.6.7_1 depends on shared library: libxtend.so - found (/usr/local/lib/libxtend.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for vcf2hap-0.1.6.7_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for vcf2hap-0.1.6.7_1 (cd /wrkdirs/usr/ports/biology/vcf2hap/work/vcf2hap-0.1.6-7-gfda1765 && /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 -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include vcf2hap.c cc -o vcf2hap vcf2hap.o -fstack-protector-strong -L{PREFIX}/lib -L/usr/local/lib -lbiolibc -lxtend =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for vcf2hap-0.1.6.7_1 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/vcf2hap/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/vcf2hap/work/stage/usr/local/share/man/man1 install -s -m 0555 vcf2hap /wrkdirs/usr/ports/biology/vcf2hap/work/stage/usr/local/bin install -m 0444 vcf2hap.1 /wrkdirs/usr/ports/biology/vcf2hap/work/stage/usr/local/share/man/man1 ====> 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=2025-05-03T04:20:04+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' '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 vcf2hap-0.1.6.7_1 ===> Building vcf2hap-0.1.6.7_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for vcf2hap-0.1.6.7_1 build of biology/vcf2hap | vcf2hap-0.1.6.7_1 ended at Sat May 3 05:20:29 BST 2025 build time: 00:00:25