=>> Building biology/minimap2 build started at Sat Sep 27 20:10:12 EDT 2025 port directory: /usr/ports/biology/minimap2 package name: minimap2-2.30 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 731 Jun 29 20:14 /usr/ports/biology/minimap2/Makefile Ports top last git commit: a936fb9b16ba Ports top unclean checkout: no Port dir last git commit: 14102a0178f9 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500064 Jail OSVERSION: 1500064 Job Id: 07 ---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/07/.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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/minimap2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/minimap2/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/minimap2/work/.cache HOME=/wrkdirs/usr/ports/biology/minimap2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/minimap2/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/minimap2/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/minimap2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/minimap2/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/minimap2/work/.cache HOME=/wrkdirs/usr/ports/biology/minimap2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/minimap2/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/minimap2/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 -DHAVE_KALLOC -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 -DHAVE_KALLOC -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/minimap2" EXAMPLESDIR="share/examples/minimap2" DATADIR="share/minimap2" WWWDIR="www/minimap2" ETCDIR="etc/minimap2" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/minimap2 DOCSDIR=/usr/local/share/doc/minimap2 EXAMPLESDIR=/usr/local/share/examples/minimap2 WWWDIR=/usr/local/www/minimap2 ETCDIR=/usr/local/etc/minimap2 --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 ===> minimap2-2.30 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.3.1.pkg [pkg.DaveG.ca] Installing pkg-2.3.1... [pkg.DaveG.ca] Extracting pkg-2.3.1: .......... done ===> minimap2-2.30 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of minimap2-2.30 =========================================================================== =================================================== ===== 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 minimap2-2.30 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by minimap2-2.30 for building => SHA256 Checksum OK for lh3-minimap2-v2.30_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 minimap2-2.30 for building ===> Extracting for minimap2-2.30 => SHA256 Checksum OK for lh3-minimap2-v2.30_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 minimap2-2.30 ===> Applying FreeBSD patches for minimap2-2.30 from /usr/ports/biology/minimap2/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> minimap2-2.30 depends on package: simde>0 - not found ===> Installing existing package /packages/All/simde-0.8.2.pkg [pkg.DaveG.ca] Installing simde-0.8.2... [pkg.DaveG.ca] Extracting simde-0.8.2: .......... done ===> minimap2-2.30 depends on package: simde>0 - found ===> Returning to build of minimap2-2.30 ===> minimap2-2.30 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [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] Extracting gmake-4.4.1: .......... done ===> minimap2-2.30 depends on package: gmake>=4.4.1 - found ===> Returning to build of minimap2-2.30 ===> minimap2-2.30 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. ===> minimap2-2.30 depends on file: /usr/local/bin/ccache - found ===> Returning to build of minimap2-2.30 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for minimap2-2.30 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for minimap2-2.30 /usr/bin/sed -i.bak -e 's|-msse4.1||g' -e 's|-msse2||g' /wrkdirs/usr/ports/biology/minimap2/work/minimap2-2.30/Makefile.simde cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include main.c -o main.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include kthread.c -o kthread.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include kalloc.c -o kalloc.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include misc.c -o misc.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include bseq.c -o bseq.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include sketch.c -o sketch.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include sdust.c -o sdust.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include options.c -o options.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include index.c -o index.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include lchain.c -o lchain.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include align.c -o align.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include hit.c -o hit.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include map.c -o map.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include format.c -o format.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include pe.c -o pe.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include seed.c -o seed.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include esterr.c -o esterr.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include splitidx.c -o splitidx.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include ksw2_extz2_sse.c -o ksw2_extz2_simde.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include ksw2_extd2_sse.c -o ksw2_extd2_simde.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include ksw2_exts2_sse.c -o ksw2_exts2_simde.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include ksw2_ll_sse.c -o ksw2_ll_simde.o cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include jump.c -o jump.o cc -D_SDUST_MAIN -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ sdust.c kalloc.o -o sdust -lz cc -c -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include example.c -o example.o ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o map.o format.o pe.o seed.o esterr.o splitidx.o ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o jump.o cc -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread cc -O2 -pipe -DHAVE_KALLOC -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ example.o -o minimap2-lite -L. -lminimap2 -lm -lz -lpthread =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for minimap2-2.30 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin mkdir -p /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/share/man/man1 mkdir -p /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/share/minimap2 install -c minimap2 /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin install -c minimap2-lite /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin install -c sdust /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin install -c minimap2.1 /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/share/man/man1 cp -R test /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/share/minimap2 strip /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin/minimap2 strip /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin/minimap2-lite strip /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin/sdust ====> 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=2025-09-28T00:10:12+0000' 'PKG_NOTE_ports_top_git_hash=a936fb9b16ba' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=14102a0178f9' '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 minimap2-2.30 ===> Building minimap2-2.30 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for minimap2-2.30 build of biology/minimap2 | minimap2-2.30 ended at Sat Sep 27 20:10:55 EDT 2025 build time: 00:00:48