=>> Building biology/bowtie2 build started at Sun Nov 9 22:30:20 EST 2025 port directory: /usr/ports/biology/bowtie2 package name: bowtie2-2.5.4 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 1586 Aug 27 2024 /usr/ports/biology/bowtie2/Makefile Ports top last git commit: ec159283c191 Ports top unclean checkout: no Port dir last git commit: 4503f388135a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500064 Job Id: 14 ---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/14/.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--- ===> The following configuration options are available for bowtie2-2.5.4: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie2/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bowtie2/work/.cache HOME=/wrkdirs/usr/ports/biology/bowtie2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bowtie2/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bowtie2/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-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie2/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bowtie2/work/.cache HOME=/wrkdirs/usr/ports/biology/bowtie2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bowtie2/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bowtie2/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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -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-- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.42 DOCSDIR="share/doc/bowtie2" EXAMPLESDIR="share/examples/bowtie2" DATADIR="share/bowtie2" WWWDIR="www/bowtie2" ETCDIR="etc/bowtie2" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bowtie2 DOCSDIR=/usr/local/share/doc/bowtie2 EXAMPLESDIR=/usr/local/share/examples/bowtie2 WWWDIR=/usr/local/www/bowtie2 ETCDIR=/usr/local/etc/bowtie2 --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 ===> bowtie2-2.5.4 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 ===> bowtie2-2.5.4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bowtie2-2.5.4 =========================================================================== =================================================== ===== 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 bowtie2-2.5.4 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bowtie2-2.5.4 for building => SHA256 Checksum OK for BenLangmead-bowtie2-v2.5.4_GH0.tar.gz. => SHA256 Checksum OK for simd-everywhere-simde-no-tests-f6a0b3b_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 bowtie2-2.5.4 for building ===> Extracting for bowtie2-2.5.4 => SHA256 Checksum OK for BenLangmead-bowtie2-v2.5.4_GH0.tar.gz. => SHA256 Checksum OK for simd-everywhere-simde-no-tests-f6a0b3b_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 bowtie2-2.5.4 ===> Applying FreeBSD patches for bowtie2-2.5.4 from /usr/ports/biology/bowtie2/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bowtie2-2.5.4 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 ===> bowtie2-2.5.4 depends on package: gmake>=4.4.1 - found ===> Returning to build of bowtie2-2.5.4 ===> bowtie2-2.5.4 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.14.pkg [pkg.DaveG.ca] Installing python311-3.11.14... [pkg.DaveG.ca] `-- Installing libffi-3.5.1... [pkg.DaveG.ca] `-- Extracting libffi-3.5.1: .......... done [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 ===== 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 ===> bowtie2-2.5.4 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of bowtie2-2.5.4 ===> bowtie2-2.5.4 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. ===> bowtie2-2.5.4 depends on file: /usr/local/bin/ccache - found ===> Returning to build of bowtie2-2.5.4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for bowtie2-2.5.4 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for bowtie2-2.5.4 c++ -DCOMPILER_OPTIONS="\" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \"" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG \ -isystem /usr/local/include -I third_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -L/usr/local/lib -lpthread -lz c++ -DCOMPILER_OPTIONS="\" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \"" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG \ -isystem /usr/local/include -I third_party \ -o bowtie2-build-l bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -L/usr/local/lib -lpthread -lz c++ -DCOMPILER_OPTIONS="\" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG \ -isystem /usr/local/include -I third_party \ -o bowtie2-align-s bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -L/usr/local/lib -lpthread -lz c++ -DCOMPILER_OPTIONS="\" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG \ -isystem /usr/local/include -I third_party \ -o bowtie2-align-l bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -L/usr/local/lib -lpthread -lz c++ \ -DCOMPILER_OPTIONS="\" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN \ -isystem /usr/local/include -I third_party \ -o bowtie2-inspect-s bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -L/usr/local/lib -lpthread -lz c++ \ -DCOMPILER_OPTIONS="\" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -Wall -Wno-unused-but-set-variable -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -DBOWTIE_64BIT_INDEX \ -isystem /usr/local/include -I third_party \ -o bowtie2-inspect-l bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -L/usr/local/lib -lpthread -lz =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bowtie2-2.5.4 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.3.3_2.pkg [pkg.DaveG.ca] Installing bash-5.3.3_2... [pkg.DaveG.ca] Extracting bash-5.3.3_2: .......... done ===> bowtie2-2.5.4 depends on executable: bash - found ===> Returning to build of bowtie2-2.5.4 ===> bowtie2-2.5.4 depends on file: /usr/local/bin/python3.11 - found ===> bowtie2-2.5.4 depends on package: perl5>=5.42.r<5.43 - not found ===> Installing existing package /packages/All/perl5-5.42.0_1.pkg [pkg.DaveG.ca] Installing perl5-5.42.0_1... [pkg.DaveG.ca] Extracting perl5-5.42.0_1: .......... done ===> bowtie2-2.5.4 depends on package: perl5>=5.42.r<5.43 - found ===> Returning to build of bowtie2-2.5.4 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for bowtie2-2.5.4 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/bowtie2/work/stage/usr/local/bin for file in bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-inspect bowtie2-build bowtie2 ; do \ cp -f $file /wrkdirs/usr/ports/biology/bowtie2/work/stage/usr/local/bin ; \ done install -s -m 555 /wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-2.5.4/bowtie2*-s /wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-2.5.4/bowtie2*-l /wrkdirs/usr/ports/biology/bowtie2/work/stage/usr/local/bin install -m 555 /wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-2.5.4/scripts/*.sh /wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-2.5.4/scripts/*.pl /wrkdirs/usr/ports/biology/bowtie2/work/stage/usr/local/share/bowtie2/scripts install -m 555 /wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-test /wrkdirs/usr/ports/biology/bowtie2/work/stage/usr/local/bin (cd /wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-2.5.4/doc && /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/bowtie2/work/stage/usr/local/share/doc/bowtie2) (cd /wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-2.5.4/example && /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/bowtie2/work/stage/usr/local/share/examples/bowtie2) ====> 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=2025-11-10T03:30:21+0000' 'PKG_NOTE_ports_top_git_hash=ec159283c191' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=4503f388135a' '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 bowtie2-2.5.4 ===> Building bowtie2-2.5.4 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for bowtie2-2.5.4 build of biology/bowtie2 | bowtie2-2.5.4 ended at Sun Nov 9 22:33:36 EST 2025 build time: 00:03:17