=>> Building biology/bbmap build started at Thu Feb 19 11:41:23 EST 2026 port directory: /usr/ports/biology/bbmap package name: bbmap-39.34 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1353 Aug 25 01:03 /usr/ports/biology/bbmap/Makefile Ports top last git commit: eac71dbf758c Ports top unclean checkout: no Port dir last git commit: 5d8f84ce55c7 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 03 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 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_0_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_0_x64-HEAD-ALL/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bbmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bbmap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bbmap/work/.cache HOME=/wrkdirs/usr/ports/biology/bbmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bbmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bbmap/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/bbmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bbmap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bbmap/work/.cache HOME=/wrkdirs/usr/ports/biology/bbmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bbmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bbmap/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-- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bbmap" EXAMPLESDIR="share/examples/bbmap" DATADIR="share/bbmap" WWWDIR="www/bbmap" ETCDIR="etc/bbmap" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bbmap DOCSDIR=/usr/local/share/doc/bbmap EXAMPLESDIR=/usr/local/share/examples/bbmap WWWDIR=/usr/local/www/bbmap ETCDIR=/usr/local/etc/bbmap --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 ===> bbmap-39.34 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> bbmap-39.34 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bbmap-39.34 =========================================================================== =================================================== ===== 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 bbmap-39.34 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bbmap-39.34 for building => SHA256 Checksum OK for BBMap_39.34.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 bbmap-39.34 for building ===> Extracting for bbmap-39.34 => SHA256 Checksum OK for BBMap_39.34.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 bbmap-39.34 ===> Applying FreeBSD patches for bbmap-39.34 from /usr/ports/biology/bbmap/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for bbmap-39.34 /usr/bin/sed -i.bak -e 's|"$DIR""current/"|/usr/local/share/java/classes/bbmap|g' /wrkdirs/usr/ports/biology/bbmap/work/bbmap/*.sh /usr/bin/sed -i.bak -e 's|"$DIR""/calcmem.sh"|/usr/local/libexec/bbmap/bbmap/calcmem.sh|g' /wrkdirs/usr/ports/biology/bbmap/work/bbmap/*.sh =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bbmap-39.34 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.3.9.pkg [pkg.DaveG.ca] Installing bash-5.3.9... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [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-0.26: .......... done [pkg.DaveG.ca] Extracting bash-5.3.9: .......... done ===> bbmap-39.34 depends on executable: bash - found ===> Returning to build of bbmap-39.34 ===> bbmap-39.34 depends on executable: pbzip2 - not found ===> Installing existing package /packages/All/pbzip2-1.1.13.pkg [pkg.DaveG.ca] Installing pbzip2-1.1.13... [pkg.DaveG.ca] Extracting pbzip2-1.1.13: .... done ===> bbmap-39.34 depends on executable: pbzip2 - found ===> Returning to build of bbmap-39.34 ===> bbmap-39.34 depends on executable: pigz - not found ===> Installing existing package /packages/All/pigz-2.8.pkg [pkg.DaveG.ca] Installing pigz-2.8... [pkg.DaveG.ca] `-- Installing zopfli-1.0.3_1... [pkg.DaveG.ca] `-- Extracting zopfli-1.0.3_1: .......... done [pkg.DaveG.ca] Extracting pigz-2.8: ..... done ===> bbmap-39.34 depends on executable: pigz - found ===> Returning to build of bbmap-39.34 ===> bbmap-39.34 depends on file: /usr/local/openjdk8/bin/java - not found ===> Installing existing package /packages/All/openjdk8-8.482.08.1.pkg [pkg.DaveG.ca] Installing openjdk8-8.482.08.1... [pkg.DaveG.ca] `-- Installing alsa-lib-1.2.14... [pkg.DaveG.ca] `-- Extracting alsa-lib-1.2.14: .......... done [pkg.DaveG.ca] `-- Installing dejavu-2.37_4... [pkg.DaveG.ca] | `-- Installing fontconfig-2.17.1,1... [pkg.DaveG.ca] | | `-- Installing expat-2.7.4... [pkg.DaveG.ca] | | `-- Extracting expat-2.7.4: .......... done [pkg.DaveG.ca] | | `-- Installing freetype2-2.14.1... [pkg.DaveG.ca] | | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | | `-- Installing png-1.6.54... [pkg.DaveG.ca] | | `-- Extracting png-1.6.54: .......... done [pkg.DaveG.ca] | | `-- Extracting freetype2-2.14.1: .......... done [pkg.DaveG.ca] | `-- Extracting fontconfig-2.17.1,1: .......... done [pkg.DaveG.ca] | `-- Installing mkfontscale-1.2.3... [pkg.DaveG.ca] | | `-- Installing libfontenc-1.1.8... [pkg.DaveG.ca] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg.DaveG.ca] | `-- Extracting mkfontscale-1.2.3: .... done [pkg.DaveG.ca] `-- Extracting dejavu-2.37_4: .......... done [pkg.DaveG.ca] `-- Installing giflib-5.2.2... [pkg.DaveG.ca] `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] `-- Installing java-zoneinfo-2021.e... [pkg.DaveG.ca] `-- Extracting java-zoneinfo-2021.e: .......... done [pkg.DaveG.ca] `-- Installing javavmwrapper-2.7.10... [pkg.DaveG.ca] `-- Extracting javavmwrapper-2.7.10: .......... done [pkg.DaveG.ca] `-- Installing libX11-1.8.12,1... [pkg.DaveG.ca] | `-- Installing libxcb-1.17.0... [pkg.DaveG.ca] | | `-- Installing libXau-1.0.12... [pkg.DaveG.ca] | | `-- Extracting libXau-1.0.12: .......... done [pkg.DaveG.ca] | | `-- Installing libXdmcp-1.1.5... [pkg.DaveG.ca] | | `-- Installing xorgproto-2024.1... [pkg.DaveG.ca] | | `-- Extracting xorgproto-2024.1: .......... done [pkg.DaveG.ca] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg.DaveG.ca] | `-- Extracting libxcb-1.17.0: .......... done [pkg.DaveG.ca] `-- Extracting libX11-1.8.12,1: .......... done [pkg.DaveG.ca] `-- Installing libXext-1.3.6,1... [pkg.DaveG.ca] `-- Extracting libXext-1.3.6,1: .......... done [pkg.DaveG.ca] `-- Installing libXi-1.8.2,1... [pkg.DaveG.ca] | `-- Installing libXfixes-6.0.1... [pkg.DaveG.ca] | `-- Extracting libXfixes-6.0.1: ....... done [pkg.DaveG.ca] `-- Extracting libXi-1.8.2,1: .......... done [pkg.DaveG.ca] `-- Installing libXrender-0.9.12... [pkg.DaveG.ca] `-- Extracting libXrender-0.9.12: ....... done [pkg.DaveG.ca] `-- Installing libXt-1.3.0,1... [pkg.DaveG.ca] | `-- Installing libICE-1.1.2,1... [pkg.DaveG.ca] | `-- Extracting libICE-1.1.2,1: .......... done [pkg.DaveG.ca] | `-- Installing libSM-1.2.6,1... [pkg.DaveG.ca] | `-- Extracting libSM-1.2.6,1: ........ done [pkg.DaveG.ca] `-- Extracting libXt-1.3.0,1: .......... done [pkg.DaveG.ca] `-- Installing libXtst-1.2.5... [pkg.DaveG.ca] `-- Extracting libXtst-1.2.5: .......... done [pkg.DaveG.ca] `-- Installing libinotify-20240724_3... [pkg.DaveG.ca] `-- Extracting libinotify-20240724_3: .......... done [pkg.DaveG.ca] Extracting openjdk8-8.482.08.1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ===== Message from freetype2-2.14.1: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== 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 openjdk8-8.482.08.1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===> bbmap-39.34 depends on file: /usr/local/openjdk8/bin/java - found ===> Returning to build of bbmap-39.34 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for bbmap-39.34 ===> Generating temporary packing list install -m 555 /wrkdirs/usr/ports/biology/bbmap/work/bbmap/*.sh /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/libexec/bbmap cd /wrkdirs/usr/ports/biology/bbmap/work/bbmap/current && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/share/java/classes/bbmap install -l rs /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/libexec/bbmap/bbduk.sh /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/bin install -l rs /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/libexec/bbmap/bbnorm.sh /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/bin install -l rs /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/libexec/bbmap/dedupe.sh /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/bin install -l rs /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/libexec/bbmap/bbmap.sh /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/bin install -l rs /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/libexec/bbmap/bloomfilter.sh /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/bin install -l rs /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/libexec/bbmap/reformat.sh /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/bin install -l rs /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/libexec/bbmap/bbmerge.sh /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/bin install -l rs /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/libexec/bbmap/tadpole.sh /wrkdirs/usr/ports/biology/bbmap/work/stage/usr/local/bin ====> 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=2026-02-19T16:41:23+0000' 'PKG_NOTE_ports_top_git_hash=eac71dbf758c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=5d8f84ce55c7' '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 bbmap-39.34 ===> Building bbmap-39.34 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for bbmap-39.34 build of biology/bbmap | bbmap-39.34 ended at Thu Feb 19 11:41:52 EST 2026 build time: 00:00:30