=>> Building biology/gffread build started at Wed Mar 11 04:44:19 EDT 2026 port directory: /usr/ports/biology/gffread package name: gffread-0.12.7 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 503 Aug 27 2024 /usr/ports/biology/gffread/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: fb16dfecae4a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 10 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-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/freebsd_14_4_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_14_4_x64-HEAD-ALL/10/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_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/gffread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gffread/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gffread/work/.cache HOME=/wrkdirs/usr/ports/biology/gffread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gffread/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gffread/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/gffread/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gffread/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gffread/work/.cache HOME=/wrkdirs/usr/ports/biology/gffread/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gffread/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gffread/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-- OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gffread" EXAMPLESDIR="share/examples/gffread" DATADIR="share/gffread" WWWDIR="www/gffread" ETCDIR="etc/gffread" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gffread DOCSDIR=/usr/local/share/doc/gffread EXAMPLESDIR=/usr/local/share/examples/gffread WWWDIR=/usr/local/www/gffread ETCDIR=/usr/local/etc/gffread --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 ===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gffread-0.12.7 =========================================================================== =================================================== ===== 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 gffread-0.12.7 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gffread-0.12.7 for building => SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz. => SHA256 Checksum OK for gpertea-gclib-v0.12.7_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 gffread-0.12.7 for building ===> Extracting for gffread-0.12.7 => SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz. => SHA256 Checksum OK for gpertea-gclib-v0.12.7_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 gffread-0.12.7 ===> Applying FreeBSD patches for gffread-0.12.7 from /usr/ports/biology/gffread/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gffread-0.12.7 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-0.26... [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 gmake-4.4.1: .......... done ===> gffread-0.12.7 depends on package: gmake>=4.4.1 - found ===> Returning to build of gffread-0.12.7 ===> gffread-0.12.7 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. ===> gffread-0.12.7 depends on file: /usr/local/bin/ccache - found ===> Returning to build of gffread-0.12.7 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for gffread-0.12.7 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for gffread-0.12.7 c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GBase.cpp -o gclib/GBase.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GArgs.cpp -o gclib/GArgs.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gdna.cpp -o gclib/gdna.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/codons.cpp -o gclib/codons.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/gff.cpp -o gclib/gff.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GStr.cpp -o gclib/GStr.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gff_utils.cpp -o gff_utils.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gffread.cpp -o gffread.o gff_utils.cpp:1275:28: warning: variable 'ustrand' set but not used [-Wunused-but-set-variable] 1275 | int fstrand=0,rstrand=0,ustrand=0; | ^ gff_utils.cpp:1451:9: warning: variable 'outcounter' set but not used [-Wunused-but-set-variable] 1451 | int outcounter=0; | ^ 2 warnings generated. gclib/gff.cpp:37:12: warning: unused variable 'CLASSCODE_J_RANK' [-Wunused-const-variable] 37 | const byte CLASSCODE_J_RANK = 6; // all junctional based overlaps | ^~~~~~~~~~~~~~~~ 1 warning generated. c++ -o gffread gclib/GBase.o gclib/GArgs.o gclib/GFaSeqGet.o gclib/gdna.o gclib/codons.o gclib/gff.o gclib/GStr.o gclib/GFastaIndex.o gff_utils.o gffread.o =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for gffread-0.12.7 ===> Generating temporary packing list install -c gffread /wrkdirs/usr/ports/biology/gffread/work/stage/usr/local/bin strip /wrkdirs/usr/ports/biology/gffread/work/stage/usr/local/bin/gffread ====> 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=2026-03-11T08:44:19+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=fb16dfecae4a' '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 gffread-0.12.7 ===> Building gffread-0.12.7 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for gffread-0.12.7 build of biology/gffread | gffread-0.12.7 ended at Wed Mar 11 04:45:04 EDT 2026 build time: 00:00:47