=>> Building biology/pooler build started at Mon Nov 10 13:00:03 EST 2025 port directory: /usr/ports/biology/pooler package name: pooler-1.89 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: ssb22@cam.ac.uk Makefile datestamp: -rw-r--r-- 1 root wheel 726 Feb 7 2025 /usr/ports/biology/pooler/Makefile Ports top last git commit: ec159283c191 Ports top unclean checkout: no Port dir last git commit: 70c1cdc4a731 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500064 Job Id: 12 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500064 UNAME_v=FreeBSD 15.0-ALPHA3 1500064 UNAME_r=15.0-ALPHA3 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_c_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_c_x64-HEAD-ALL/12/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_c_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_c_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-- ssb22@cam.ac.uk --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/pooler/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pooler/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/pooler/work/.cache HOME=/wrkdirs/usr/ports/biology/pooler/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/pooler/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/pooler/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/pooler/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pooler/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/pooler/work/.cache HOME=/wrkdirs/usr/ports/biology/pooler/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/pooler/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/pooler/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 -fopenmp -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fopenmp -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=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/pooler" EXAMPLESDIR="share/examples/pooler" DATADIR="share/pooler" WWWDIR="www/pooler" ETCDIR="etc/pooler" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pooler DOCSDIR=/usr/local/share/doc/pooler EXAMPLESDIR=/usr/local/share/examples/pooler WWWDIR=/usr/local/www/pooler ETCDIR=/usr/local/etc/pooler --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 ===> pooler-1.89 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> pooler-1.89 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pooler-1.89 =========================================================================== =================================================== ===== 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 pooler-1.89 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by pooler-1.89 for building => SHA256 Checksum OK for ssb22-PrimerPooler-v1.89-gf33bf5d_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 pooler-1.89 for building ===> Extracting for pooler-1.89 => SHA256 Checksum OK for ssb22-PrimerPooler-v1.89-gf33bf5d_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 pooler-1.89 /usr/bin/sed -i.bak -e 's|man/man1|share/man/man1|g' /wrkdirs/usr/ports/biology/pooler/work/PrimerPooler-1.89-gf33bf5d/pooler/Makefile =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pooler-1.89 depends on executable: update-desktop-database - not found ===> Installing existing package /packages/All/desktop-file-utils-0.28.pkg [pkg.DaveG.ca] Installing desktop-file-utils-0.28... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] `-- Installing glib-2.84.1_3,2... [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing libiconv-1.18... [pkg.DaveG.ca] | `-- Extracting libiconv-1.18: .......... done [pkg.DaveG.ca] | `-- Installing libinotify-20240724_3... [pkg.DaveG.ca] | `-- Extracting libinotify-20240724_3: .......... done [pkg.DaveG.ca] | `-- Installing pcre2-10.46... [pkg.DaveG.ca] | `-- Extracting pcre2-10.46: .......... done [pkg.DaveG.ca] | `-- Installing py311-packaging-25.0... [pkg.DaveG.ca] | | `-- Installing python311-3.11.14... [pkg.DaveG.ca] | | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | | `-- Installing readline-8.3.1... [pkg.DaveG.ca] | | `-- Extracting readline-8.3.1: .......... done [pkg.DaveG.ca] | | `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] | `-- Extracting py311-packaging-25.0: .......... done [pkg.DaveG.ca] `-- Extracting glib-2.84.1_3,2: .......... done [pkg.DaveG.ca] Extracting desktop-file-utils-0.28: .......... done Building cache database of MIME types ==> Running trigger: desktop-file-utils.ucl Building cache database of MIME types ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from libinotify-20240724_3: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from python311-3.11.14: -- 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 ===> pooler-1.89 depends on executable: update-desktop-database - found ===> Returning to build of pooler-1.89 ===> pooler-1.89 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. ===> pooler-1.89 depends on file: /usr/local/bin/ccache - found ===> Returning to build of pooler-1.89 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for pooler-1.89 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for pooler-1.89 --- 32-64.h --- --- 128.h --- --- 32.h --- --- 32-64.h --- chmod +w 32-64.h 2>/dev/null || true --- 32.h --- chmod +w 32.h 2>/dev/null || true --- 128.h --- chmod +w 128.h 2>/dev/null || true --- 32-64.h --- sed -e s/64/32/g -e s/128/64/g < 64-128.h > 32-64.h --- 32.h --- sed -e s/64/32/g < 64.h > 32.h --- 128.h --- sed -e s/64/128/g < 64.h > 128.h --- 32-64.h --- chmod -w 32-64.h 2>/dev/null || true --- 32.h --- chmod -w 32.h 2>/dev/null || true --- 128.h --- chmod -w 128.h 2>/dev/null || true --- pooler --- $(sh -c 'case "$OSTYPE" in darwin*) [ "cc" = cc ] && gcc --version 2>/dev/null >/dev/null ;; *) false ;; esac' && echo gcc || echo "cc") -O2 -pipe -fopenmp -fstack-protector-strong -fno-strict-aliasing $(echo 'int main(){}' > _test.c; if $(sh -c 'case "$OSTYPE" in darwin*) [ "cc" = cc ] && gcc --version 2>/dev/null >/dev/null ;; *) false ;; esac' && echo gcc || echo "cc") -fopenmp _test.c -o /dev/null 2>/dev/null; then echo -fopenmp; fi; rm _test.c) *.c -o pooler -lm =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> pooler-1.89 depends on executable: update-desktop-database - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for pooler-1.89 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/pooler/work/stage//usr/local/bin mkdir -p /wrkdirs/usr/ports/biology/pooler/work/stage//usr/local/share/man/man1 cp pooler /wrkdirs/usr/ports/biology/pooler/work/stage//usr/local/bin/ cp pooler.desktop /wrkdirs/usr/ports/biology/pooler/work/stage//usr/local/share/applications cp pooler.1 /wrkdirs/usr/ports/biology/pooler/work/stage//usr/local/share/man/man1/ strip /wrkdirs/usr/ports/biology/pooler/work/stage//usr/local/bin/pooler ====> 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=2025-11-10T18:00:03+0000' 'PKG_NOTE_ports_top_git_hash=ec159283c191' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=70c1cdc4a731' '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 pooler-1.89 ===> Building pooler-1.89 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for pooler-1.89 build of biology/pooler | pooler-1.89 ended at Mon Nov 10 13:00:11 EST 2025 build time: 00:00:10