=>> Building biology/bowtie build started at Wed Jan 21 05:16:43 EST 2026 port directory: /usr/ports/biology/bowtie package name: bowtie-1.3.1 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p7 FreeBSD 14.3-RELEASE-p7 1403000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1265 Aug 27 2024 /usr/ports/biology/bowtie/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: 06df180a9e39 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 07 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p7 1403000 UNAME_r=14.3-RELEASE-p7 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_3_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_3_x64-HEAD-ALL/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_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 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=/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/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=/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 --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=/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=" " 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-- PORTDOCS="" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 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=14.3 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/bowtie" EXAMPLESDIR="share/examples/bowtie" DATADIR="share/bowtie" WWWDIR="www/bowtie" ETCDIR="etc/bowtie" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 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/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--- 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 ===> bowtie-1.3.1 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 ===> 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.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 ===> bowtie-1.3.1 depends on package: gmake>=4.4.1 - found ===> Returning to build of bowtie-1.3.1 ===> bowtie-1.3.1 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. ===> bowtie-1.3.1 depends on file: /usr/local/bin/ccache - 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="\"2026-01-21T10:16:49\"" -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 \ -lz -lpthread 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="\"2026-01-21T10:16:49\"" -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 \ -lz -lpthread 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="\"2026-01-21T10:16:49\"" -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 \ -lz -lpthread 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="\"2026-01-21T10:16:49\"" -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 \ -lz -lpthread 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="\"2026-01-21T10:16:49\"" -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 \ -lz -lpthread 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="\"2026-01-21T10:16:49\"" -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 \ -lz -lpthread In file included from ebwt_build.cpp:8: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ In file included from ebwt_build.cpp:8: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:25: In file included from ./blockwise_sa.h:17: ./diff_sample.h:464:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 464 | size_t amapEnts = 1; | ^ In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:25: In file included from ./blockwise_sa.h:17: ./diff_sample.h:464:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 464 | size_t amapEnts = 1; | ^ ./diff_sample.h:669:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 669 | TIndexOffU added = 0; | ^ ./diff_sample.h:669:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] ./diff_sample.h:738:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 738 | TIndexOffU added = 0; | ^ 669 | TIndexOffU added = 0; | ^ ./diff_sample.h:738:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 738 | TIndexOffU added = 0; | ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:17: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:17: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ In file included from bowtie_inspect.cpp:7: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ In file included from bowtie_inspect.cpp:7: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: In file included from ./ebwt.h:25: In file included from ./blockwise_sa.h:17: ./diff_sample.h:464:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 464 | size_t amapEnts = 1; | ^ ./diff_sample.h:669:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 669 | TIndexOffU added = 0; | ^ ./diff_sample.h:738:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 738 | TIndexOffU added = 0; | ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: In file included from ./ebwt.h:25: In file included from ./blockwise_sa.h:17: ./diff_sample.h:464:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 464 | size_t amapEnts = 1; | ^ ./diff_sample.h:669:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 669 | TIndexOffU added = 0; | ^ ./diff_sample.h:738:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 738 | TIndexOffU added = 0; | ^ 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] 70 | uint32_t qual = 0; | ^ 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] 70 | uint32_t qual = 0; | ^ In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:1525: ./ebwt_search_backtrack.h:1245:24: warning: variable 'hiHalfMms' set but not used [-Wunused-but-set-variable] 1245 | int loHalfMms = 0, hiHalfMms = 0; | ^ ./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable] 1674 | uint32_t cumSz = 0; | ^ ./ebwt_search_backtrack.h:1675:12: warning: variable 'eligiblesVisited' set but not used [-Wunused-but-set-variable] 1675 | uint32_t eligiblesVisited = 0; | ^ In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:1525: ./ebwt_search_backtrack.h:1245:24: warning: variable 'hiHalfMms' set but not used [-Wunused-but-set-variable] 1245 | int loHalfMms = 0, hiHalfMms = 0; | ^ ./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable] 1674 | uint32_t cumSz = 0; | ^ ./ebwt_search_backtrack.h:1675:12: warning: variable 'eligiblesVisited' set but not used [-Wunused-but-set-variable] 1675 | uint32_t eligiblesVisited = 0; | ^ ./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable] 2726 | uint32_t sLeft = s >> 1; | ^ ./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable] 2726 | uint32_t sLeft = s >> 1; | ^ In file included from ebwt_build.cpp:10: ./ebwt.h:2791:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable] 2791 | TIndexOffU restOff = 0; | ^ 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] 70 | uint32_t qual = 0; | ^ In file included from ebwt_build.cpp:10: ./ebwt.h:2791:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable] 2791 | TIndexOffU restOff = 0; | ^ 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] 70 | uint32_t qual = 0; | ^ ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] 3890 | TIndexOffU patoff = 0; | ^ ./ebwt.h:3882:13: warning: variable 'seqsRead' set but not used [-Wunused-but-set-variable] 3882 | TIndexOffU seqsRead = 0; | ^ ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] 3890 | TIndexOffU patoff = 0; | ^ ./ebwt.h:3882:13: warning: variable 'seqsRead' set but not used [-Wunused-but-set-variable] 3882 | TIndexOffU seqsRead = 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:1245:24: warning: variable 'hiHalfMms' set but not used [-Wunused-but-set-variable] 1245 | int loHalfMms = 0, hiHalfMms = 0; | ^ ./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable] 1674 | uint32_t cumSz = 0; | ^ ./ebwt_search_backtrack.h:1675:12: warning: variable 'eligiblesVisited' set but not used [-Wunused-but-set-variable] 1675 | uint32_t eligiblesVisited = 0; | ^ ./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable] 2726 | uint32_t sLeft = s >> 1; | ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: ./ebwt.h:2791:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable] 2791 | TIndexOffU restOff = 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:1245:24: warning: variable 'hiHalfMms' set but not used [-Wunused-but-set-variable] 1245 | int loHalfMms = 0, hiHalfMms = 0; | ^ ./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable] 1674 | uint32_t cumSz = 0; | ^ ./ebwt_search_backtrack.h:1675:12: warning: variable 'eligiblesVisited' set but not used [-Wunused-but-set-variable] 1675 | uint32_t eligiblesVisited = 0; | ^ ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] 3890 | TIndexOffU patoff = 0; | ^ ./ebwt.h:3882:13: warning: variable 'seqsRead' set but not used [-Wunused-but-set-variable] 3882 | TIndexOffU seqsRead = 0; | ^ ./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable] 2726 | uint32_t sLeft = s >> 1; | ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: ./ebwt.h:2791:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable] 2791 | TIndexOffU restOff = 0; | ^ ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] 3890 | TIndexOffU patoff = 0; | ^ ./ebwt.h:3882:13: warning: variable 'seqsRead' set but not used [-Wunused-but-set-variable] 3882 | TIndexOffU seqsRead = 0; | ^ ebwt_search.cpp:1359:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1359 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/comp.h:40:12: note: read of non-const variable 'nthreads' is not allowed in a constant expression 40 | return __lhs < __rhs; | ^ /usr/include/c++/v1/__algorithm/max.h:30:10: note: in call to '__comp.operator()(nthreads, thread_ceiling)' 30 | return __comp(__a, __b) ? __b : __a; | ^~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/max.h:36:10: note: in call to 'max>(nthreads, thread_ceiling, {})' 36 | return std::max(__a, __b, __less<>()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:1359:11: note: in call to 'max(nthreads, thread_ceiling)' 1359 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:85:12: note: declared here 85 | static int nthreads; // number of pthreads operating concurrently | ^ ebwt_search.cpp:1426:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] 1426 | int orig_threads = nthreads, steal_ctr = 1; | ^ ebwt_search.cpp:1739:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1739 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/comp.h:40:12: note: read of non-const variable 'nthreads' is not allowed in a constant expression 40 | return __lhs < __rhs; | ^ /usr/include/c++/v1/__algorithm/max.h:30:10: note: in call to '__comp.operator()(nthreads, thread_ceiling)' 30 | return __comp(__a, __b) ? __b : __a; | ^~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/max.h:36:10: note: in call to 'max>(nthreads, thread_ceiling, {})' 36 | return std::max(__a, __b, __less<>()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:1739:11: note: in call to 'max(nthreads, thread_ceiling)' 1739 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:85:12: note: declared here 85 | static int nthreads; // number of pthreads operating concurrently | ^ ebwt_search.cpp:1807:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] 1807 | int orig_threads = nthreads, steal_ctr = 1; | ^ ebwt_search.cpp:2235:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 2235 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/comp.h:40:12: note: read of non-const variable 'nthreads' is not allowed in a constant expression 40 | return __lhs < __rhs; | ^ /usr/include/c++/v1/__algorithm/max.h:30:10: note: in call to '__comp.operator()(nthreads, thread_ceiling)' 30 | return __comp(__a, __b) ? __b : __a; | ^~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/max.h:36:10: note: in call to 'max>(nthreads, thread_ceiling, {})' 36 | return std::max(__a, __b, __less<>()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:2235:11: note: in call to 'max(nthreads, thread_ceiling)' 2235 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:85:12: note: declared here 85 | static int nthreads; // number of pthreads operating concurrently | ^ ebwt_search.cpp:2303:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] 2303 | int orig_threads = nthreads, steal_ctr = 1; | ^ ebwt_search.cpp:2773:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 2773 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/comp.h:40:12: note: read of non-const variable 'nthreads' is not allowed in a constant expression 40 | return __lhs < __rhs; | ^ /usr/include/c++/v1/__algorithm/max.h:30:10: note: in call to '__comp.operator()(nthreads, thread_ceiling)' 30 | return __comp(__a, __b) ? __b : __a; | ^~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/max.h:36:10: note: in call to 'max>(nthreads, thread_ceiling, {})' 36 | return std::max(__a, __b, __less<>()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:2773:11: note: in call to 'max(nthreads, thread_ceiling)' 2773 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:85:12: note: declared here 85 | static int nthreads; // number of pthreads operating concurrently | ^ ebwt_search.cpp:2849:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] 2849 | int orig_threads = nthreads, steal_ctr = 1; | ^ ebwt_search.cpp:1359:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1359 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/comp.h:40:12: note: read of non-const variable 'nthreads' is not allowed in a constant expression 40 | return __lhs < __rhs; | ^ /usr/include/c++/v1/__algorithm/max.h:30:10: note: in call to '__comp.operator()(nthreads, thread_ceiling)' 30 | return __comp(__a, __b) ? __b : __a; | ^~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/max.h:36:10: note: in call to 'max>(nthreads, thread_ceiling, {})' 36 | return std::max(__a, __b, __less<>()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:1359:11: note: in call to 'max(nthreads, thread_ceiling)' 1359 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:85:12: note: declared here 85 | static int nthreads; // number of pthreads operating concurrently | ^ ebwt_search.cpp:1426:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] 1426 | int orig_threads = nthreads, steal_ctr = 1; | ^ ebwt_search.cpp:1739:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 1739 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/comp.h:40:12: note: read of non-const variable 'nthreads' is not allowed in a constant expression 40 | return __lhs < __rhs; | ^ /usr/include/c++/v1/__algorithm/max.h:30:10: note: in call to '__comp.operator()(nthreads, thread_ceiling)' 30 | return __comp(__a, __b) ? __b : __a; | ^~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/max.h:36:10: note: in call to 'max>(nthreads, thread_ceiling, {})' 36 | return std::max(__a, __b, __less<>()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:1739:11: note: in call to 'max(nthreads, thread_ceiling)' 1739 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:85:12: note: declared here 85 | static int nthreads; // number of pthreads operating concurrently | ^ ebwt_search.cpp:1807:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] 1807 | int orig_threads = nthreads, steal_ctr = 1; | ^ ebwt_search.cpp:2235:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 2235 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/comp.h:40:12: note: read of non-const variable 'nthreads' is not allowed in a constant expression 40 | return __lhs < __rhs; | ^ /usr/include/c++/v1/__algorithm/max.h:30:10: note: in call to '__comp.operator()(nthreads, thread_ceiling)' 30 | return __comp(__a, __b) ? __b : __a; | ^~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/max.h:36:10: note: in call to 'max>(nthreads, thread_ceiling, {})' 36 | return std::max(__a, __b, __less<>()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:2235:11: note: in call to 'max(nthreads, thread_ceiling)' 2235 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:85:12: note: declared here 85 | static int nthreads; // number of pthreads operating concurrently | ^ ebwt_search.cpp:2303:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] 2303 | int orig_threads = nthreads, steal_ctr = 1; | ^ ebwt_search.cpp:2773:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 2773 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/comp.h:40:12: note: read of non-const variable 'nthreads' is not allowed in a constant expression 40 | return __lhs < __rhs; | ^ /usr/include/c++/v1/__algorithm/max.h:30:10: note: in call to '__comp.operator()(nthreads, thread_ceiling)' 30 | return __comp(__a, __b) ? __b : __a; | ^~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/max.h:36:10: note: in call to 'max>(nthreads, thread_ceiling, {})' 36 | return std::max(__a, __b, __less<>()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:2773:11: note: in call to 'max(nthreads, thread_ceiling)' 2773 | int tids[max(nthreads, thread_ceiling)]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ebwt_search.cpp:85:12: note: declared here 85 | static int nthreads; // number of pthreads operating concurrently | ^ ebwt_search.cpp:2849:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] 2849 | int orig_threads = nthreads, steal_ctr = 1; | ^ In file included from bowtie_inspect.cpp:9: In file included from ./ebwt.h:25: In file included from ./blockwise_sa.h:17: ./diff_sample.h:464:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 464 | size_t amapEnts = 1; | ^ In file included from bowtie_inspect.cpp:9: In file included from ./ebwt.h:25: In file included from ./blockwise_sa.h:17: ./diff_sample.h:464:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 464 | size_t amapEnts = 1; | ^ In file included from bowtie_inspect.cpp:9: In file included from ./ebwt.h:1525: ./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable] 2726 | uint32_t sLeft = s >> 1; | ^ In file included from bowtie_inspect.cpp:9: In file included from ./ebwt.h:1525: ./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable] 2726 | uint32_t sLeft = s >> 1; | ^ In file included from bowtie_inspect.cpp:9: ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] 3890 | TIndexOffU patoff = 0; | ^ In file included from bowtie_inspect.cpp:9: ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] 3890 | TIndexOffU patoff = 0; | ^ 12 warnings generated. 12 warnings generated. In file included from ref_read.cpp:2: In file included from ./ref_read.h:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. 4 warnings generated. In file included from ref_read.cpp:2: In file included from ./ref_read.h:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. 4 warnings generated. In file included from ref_read.cpp:2: In file included from ./ref_read.h:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. 20 warnings generated. 20 warnings generated. In file included from ref_read.cpp:2: In file included from ./ref_read.h:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. In file included from ref_read.cpp:2: In file included from ./ref_read.h:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ In file included from ref_read.cpp:2: In file included from ./ref_read.h:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. 1 warning generated. In file included from bowtie_build_main.cpp:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. In file included from bowtie_build_main.cpp:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. In file included from pat.cpp:10: In file included from ./pat.h:17: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ In file included from pat.cpp:10: In file included from ./pat.h:17: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. 1 warning generated. In file included from ebwt_search_util.cpp:1: In file included from ./ebwt_search_util.h:8: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 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] 70 | uint32_t qual = 0; | ^ In file included from ebwt_search_util.cpp:1: In file included from ./ebwt_search_util.h:8: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 2 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] 70 | uint32_t qual = 0; | ^ 2 warnings generated. In file included from hit_set.cpp:11: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. In file included from hit_set.cpp:11: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. In file included from sam.cpp:8: In file included from ./hit.h:16: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ In file included from sam.cpp:8: In file included from ./hit.h:16: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. 1 warning generated. In file included from hit.cpp:1: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ In file included from hit.cpp:1: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. 1 warning generated. In file included from bowtie_main.cpp:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 0; | ^ 1 warning generated. In file included from bowtie_main.cpp:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4077 | int thru = 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/python3.11 - 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-8.3.3... [pkg.DaveG.ca] `-- Extracting readline-8.3.3: .......... 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 ===> bowtie-1.3.1 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of bowtie-1.3.1 ===> bowtie-1.3.1 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 ===> bowtie-1.3.1 depends on package: perl5>=5.42.r<5.43 - 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=2026-01-21T10:16:44+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=06df180a9e39' '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 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 Wed Jan 21 05:18:06 EST 2026 build time: 00:01:25