=>> Building biology/bowtie build started at Tue Apr 2 14:42:58 BST 2024 port directory: /usr/ports/biology/bowtie package name: bowtie-1.3.1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1265 Nov 6 13:35 /usr/ports/biology/bowtie/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 06df180a9e Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 19 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/19/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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 bowtie-1.3.1: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=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/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bowtie/work/.cache HOME=/wrkdirs/usr/ports/biology/bowtie/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/bowtie/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bowtie/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bowtie/work/.cache HOME=/wrkdirs/usr/ports/biology/bowtie/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/bowtie/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bowtie/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=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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="" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 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/5.36 DOCSDIR="share/doc/bowtie" EXAMPLESDIR="share/examples/bowtie" DATADIR="share/bowtie" WWWDIR="www/bowtie" ETCDIR="etc/bowtie" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bowtie DOCSDIR=/usr/local/share/doc/bowtie EXAMPLESDIR=/usr/local/share/examples/bowtie WWWDIR=/usr/local/www/bowtie ETCDIR=/usr/local/etc/bowtie --End SUB_LIST-- ---Begin make.conf--- 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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 --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 ===> bowtie-1.3.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> bowtie-1.3.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bowtie-1.3.1 =========================================================================== =================================================== ===== 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 bowtie-1.3.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bowtie-1.3.1 for building => SHA256 Checksum OK for BenLangmead-bowtie-v1.3.1_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 bowtie-1.3.1 for building ===> Extracting for bowtie-1.3.1 => SHA256 Checksum OK for BenLangmead-bowtie-v1.3.1_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 bowtie-1.3.1 ===> Applying FreeBSD patches for bowtie-1.3.1 from /usr/ports/biology/bowtie/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bowtie-1.3.1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> bowtie-1.3.1 depends on package: gmake>=4.4.1 - found ===> Returning to build of bowtie-1.3.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for bowtie-1.3.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for bowtie-1.3.1 c++ -DCOMPILER_OPTIONS="\" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2024-04-02T13:43:03\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party \ -o bowtie-build-s ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp bowtie_build_main.cpp \ -fstack-protector-strong -lz -lpthread In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:1525: In file included from ./ebwt_search_backtrack.h:8: ./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable] uint32_t qual = 0; ^ In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:1525: ./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable] uint32_t cumSz = 0; ^ In file included from ebwt_build.cpp:10: ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 3 warnings generated. c++ -DCOMPILER_OPTIONS="\" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2024-04-02T13:43:24\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party \ -o bowtie-build-l ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp bowtie_build_main.cpp \ -fstack-protector-strong -lz -lpthread In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:1525: In file included from ./ebwt_search_backtrack.h:8: ./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable] uint32_t qual = 0; ^ In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:1525: ./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable] uint32_t cumSz = 0; ^ In file included from ebwt_build.cpp:10: ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 3 warnings generated. c++ -DCOMPILER_OPTIONS="\" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2024-04-02T13:43:44\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party \ -o bowtie-align-s ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \ -fstack-protector-strong -lz -lpthread In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: In file included from ./ebwt.h:1525: In file included from ./ebwt_search_backtrack.h:8: ./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable] uint32_t qual = 0; ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: In file included from ./ebwt.h:1525: ./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable] uint32_t cumSz = 0; ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 3 warnings generated. In file included from ebwt_search_util.cpp:1: ./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable] uint32_t qual = 0; ^ 1 warning generated. c++ -DCOMPILER_OPTIONS="\" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2024-04-02T13:44:27\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party \ -o bowtie-align-l ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \ -fstack-protector-strong -lz -lpthread In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: In file included from ./ebwt.h:1525: In file included from ./ebwt_search_backtrack.h:8: ./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable] uint32_t qual = 0; ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: In file included from ./ebwt.h:1525: ./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable] uint32_t cumSz = 0; ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 3 warnings generated. In file included from ebwt_search_util.cpp:1: ./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable] uint32_t qual = 0; ^ 1 warning generated. c++ \ -DCOMPILER_OPTIONS="\" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2024-04-02T13:45:09\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party -I . \ -o bowtie-inspect-s bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp \ -fstack-protector-strong -lz -lpthread In file included from bowtie_inspect.cpp:9: ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. c++ \ -DCOMPILER_OPTIONS="\" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector-strong -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2024-04-02T13:45:31\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party -I . \ -o bowtie-inspect-l bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp \ -fstack-protector-strong -lz -lpthread In file included from bowtie_inspect.cpp:9: ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bowtie-1.3.1 depends on file: /usr/local/bin/python3.9 - not found ===> Installing existing package /packages/All/python39-3.9.18_1.pkg [pkg-builder.dan.net.uk] Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] Extracting python39-3.9.18_1: .......... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> bowtie-1.3.1 depends on file: /usr/local/bin/python3.9 - found ===> Returning to build of bowtie-1.3.1 ===> bowtie-1.3.1 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_1.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_1: .......... done ===> bowtie-1.3.1 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of bowtie-1.3.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for bowtie-1.3.1 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin for file in bowtie-build-s bowtie-build-l bowtie-align-s bowtie-align-l bowtie-inspect-s bowtie-inspect-l bowtie-inspect bowtie-build bowtie ; do \ cp -f $file /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin ; \ done /bin/mkdir -p /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/bowtie/scripts install -m 555 /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.3.1/bowtie /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.3.1/bowtie-build /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.3.1/bowtie-inspect /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin install -m 555 /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.3.1/scripts/*.sh /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.3.1/scripts/*.pl /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/bowtie/scripts cd /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.3.1 && /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 'genomes indexes reads' /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/bowtie cd /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.3.1/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/bowtie/work/stage/usr/local/share/doc/bowtie /usr/bin/strip /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin/*-[sl] ====> 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=2024-04-02T13:42:58+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=06df180a9e' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for bowtie-1.3.1 ===> Building bowtie-1.3.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for bowtie-1.3.1 build of biology/bowtie | bowtie-1.3.1 ended at Tue Apr 2 14:46:11 BST 2024 build time: 00:03:14