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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/ampere5/data/143arm64-default/8205a98493ef/logs/py311-pysam-0.23.0_1.log Build URL: https://pkg-status.freebsd.org/ampere5/build.html?mastername=143arm64-default&build=8205a98493ef Log: =>> Building biology/py-pysam build started at Tue Feb 10 15:00:58 UTC 2026 port directory: /usr/ports/biology/py-pysam package name: py311-pysam-0.23.0_1 building for: FreeBSD 143arm64-default-job-19 14.3-RELEASE-p8 FreeBSD 14.3-RELEASE-p8 arm64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 1128 Jan 3 01:01 /usr/ports/biology/py-pysam/Makefile Ports top last git commit: 8205a98493ef24a661b0afb0726cfca7b24312cb Ports top unclean checkout: no Port dir last git commit: a633e739157c8cf87492b7c95e3725b84bb51dc8 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4-15-g61aba751 Host OSVERSION: 1600007 Jail OSVERSION: 1403000 Job Id: 19 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p8 UNAME_r=14.3-RELEASE-p8 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=3.4.4-15-g61aba751 MASTERMNT=/usr/local/poudriere/data/.m/143arm64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/143arm64-default/19/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=143arm64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/143arm64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4-15-g61aba751 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py311 MAKE_ARGS= FLAVOR=py311 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pysam/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-pysam/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- HTSLIB_MODE=external HTSLIB_LIBRARY_DIR=/usr/local/lib HTSLIB_INCLUDE_DIR=/usr/local/include XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pysam/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-pysam/work-py311/.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 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= 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-- 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 DOCSDIR="share/doc/pysam" EXAMPLESDIR="share/examples/pysam" DATADIR="share/pysam" WWWDIR="www/pysam" ETCDIR="etc/pysam" --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/pysam DOCSDIR=/usr/local/share/doc/pysam EXAMPLESDIR=/usr/local/share/examples/pysam WWWDIR=/usr/local/www/pysam ETCDIR=/usr/local/etc/pysam --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### 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) 1048576 stack size (kbytes, -s) 1048576 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-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pysam-0.23.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [143arm64-default-job-19] Installing pkg-2.5.1... [143arm64-default-job-19] Extracting pkg-2.5.1: .......... done ===> py311-pysam-0.23.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-pysam-0.23.0_1 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by py311-pysam-0.23.0_1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by py311-pysam-0.23.0_1 for building => SHA256 Checksum OK for pysam-developers-pysam-v0.23.0_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by py311-pysam-0.23.0_1 for building ===> Extracting for py311-pysam-0.23.0_1 => SHA256 Checksum OK for pysam-developers-pysam-v0.23.0_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py311-pysam-0.23.0_1 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pysam-0.23.0_1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [143arm64-default-job-19] Installing gmake-4.4.1... [143arm64-default-job-19] `-- Installing gettext-runtime-0.26... [143arm64-default-job-19] | `-- Installing indexinfo-0.3.1_1... [143arm64-default-job-19] | `-- Extracting indexinfo-0.3.1_1: .... done [143arm64-default-job-19] `-- Extracting gettext-runtime-0.26: .......... done [143arm64-default-job-19] Extracting gmake-4.4.1: .......... done ===> py311-pysam-0.23.0_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of py311-pysam-0.23.0_1 ===> py311-pysam-0.23.0_1 depends on package: py311-cython>=3.2.4 - not found ===> Installing existing package /packages/All/py311-cython-3.2.4.pkg [143arm64-default-job-19] Installing py311-cython-3.2.4... [143arm64-default-job-19] `-- Installing python311-3.11.14_2... [143arm64-default-job-19] | `-- Installing libffi-3.5.1... [143arm64-default-job-19] | `-- Extracting libffi-3.5.1: .......... done [143arm64-default-job-19] | `-- Installing mpdecimal-4.0.1... [143arm64-default-job-19] | `-- Extracting mpdecimal-4.0.1: .......... done [143arm64-default-job-19] | `-- Installing readline-8.3.3... [143arm64-default-job-19] | `-- Extracting readline-8.3.3: .......... done [143arm64-default-job-19] `-- Extracting python311-3.11.14_2: .......... done [143arm64-default-job-19] Extracting py311-cython-3.2.4: .......... done ===== Message from python311-3.11.14_2: -- <snip> creating build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311 creating build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/htslib_util.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libchtslib.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/htslib_util.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libchtslib.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -L/usr/local/lib -lz -lhts -o build/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libchtslib.cpython-311.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension Compiling pysam/libcsamtools.pyx because it changed. [1/1] Cythonizing pysam/libcsamtools.pyx building 'pysam.libcsamtools' extension creating build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools creating build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/lz4 cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libcsamtools.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/amplicon_stats.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam2depth.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_addrprg.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_aux.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_cat.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_color.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_consensus.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_fastq.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_flags.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_import.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_index.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_lpileup.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_markdup.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_mate.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_md.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_plbuf.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_plcmd.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_reheader.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_rmdup.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_samples.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_sort.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_split.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bam_stat.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bamshuf.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bamtk.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bamtk.c.pysam.c:314:9: warning: code will never be executed [-Wunreachable-code] 314 | print_error_errno(argv[1], "closing standard output failed"); | ^~~~~~~~~~~~~~~~~ samtools/bamtk.c.pysam.c:313:9: note: silence by adding parentheses to mark code as explicitly dead 313 | if (0) { //if (fclose(samtools_stdout) != 0 && errno != EBADF) { | ^ | /* DISABLES CODE */ ( ) 1 warning generated. cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bedcov.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/bedidx.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/consensus_pileup.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/coverage.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/cram_size.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/cut_target.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/dict.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/faidx.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/lz4/lz4.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/padding.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/phase.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/reference.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/reset.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/sam_opts.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/sam_utils.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/sam_view.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/sample.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/samtools.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/stats.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/stats_isize.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c samtools/tmp_file.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcsamtools.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/amplicon_stats.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam2depth.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_addrprg.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_ampliconclip.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_aux.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_cat.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_color.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_consensus.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_fastq.c.pysam.o build/temp.freebsd-1 4.3-RELEASE-p8-arm64-cpython-311/samtools/bam_flags.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_import.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_index.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_lpileup.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_markdup.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_mate.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_md.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_plbuf.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_plcmd.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_quickcheck.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_reheader.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_rmdup.c.pysam.o build/temp.freeb sd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_rmdupse.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_samples.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_sort.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_split.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bam_stat.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bamshuf.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bamtk.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bedcov.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/bedidx.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/consensus_pileup.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/coverage.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/cram_size.c.pysam.o build/temp.freebsd-14.3-R ELEASE-p8-arm64-cpython-311/samtools/cut_target.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/dict.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/faidx.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/lz4/lz4.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/padding.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/phase.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/reference.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/reset.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/sam_opts.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/sam_utils.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/sam_view.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/sample.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/s amtools.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/stats.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/stats_isize.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/samtools/tmp_file.c.pysam.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -o build/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcsamtools.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcftools.pyx because it changed. [1/1] Cythonizing pysam/libcbcftools.pyx building 'pysam.libcbcftools' extension creating build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/HMM.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/abuf.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/bam2bcf.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/bam2bcf_edlib.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bam2bcf_edlib.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/bam_sample.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/bcftools.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/bin.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/ccall.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/cols.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/consensus.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/convert.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/convert.c.pysam.c:541:66: warning: code will never be executed [-Wunreachable-code] 541 | default: error("Unexpected type: %d\n", fmt->fmt->type); bcftools_exit(1); break; | ^~~~~~~~~~~~~ 1 warning generated. cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/csq.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/dist.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/edlib.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/edlib.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/em.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/extsort.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/filter.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/filter.c.pysam.c:3911:12: warning: code will never be executed [-Wunreachable-code] 3911 | if (0) filter_debug_print(out, NULL, nout); | ^~~~~~~~~~~~~~~~~~ bcftools/filter.c.pysam.c:3911:9: note: silence by adding parentheses to mark code as explicitly dead 3911 | if (0) filter_debug_print(out, NULL, nout); | ^ | /* DISABLES CODE */ ( ) 1 warning generated. cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/gff.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/gff.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/gvcf.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/hclust.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/kmin.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/main.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/mcall.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/mpileup.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/ploidy.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/prob1.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/read_consensus.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/regidx.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/reheader.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/str_finder.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/tabix.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/tabix.c.pysam.c:58:22: warning: code will never be executed [-Wunreachable-code] 58 | detect = 0; | ^ 1 warning generated. cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfannotate.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfbuf.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfcall.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfcnv.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfconcat.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfconvert.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcffilter.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfgtcheck.c.pysam.c:1376:39: warning: code will never be executed [-Wunreachable-code] 1376 | args->min_inter_err = strtod(optarg,&tmp); | ^~~~~~ 1 warning generated. cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfhead.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfindex.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfisec.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfmerge.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfnorm.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfplugin.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfquery.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfroh.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfsom.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfsort.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfstats.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcfview.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/vcmp.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c bcftools/version.c.pysam.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libcbcftools.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/HMM.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/abuf.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bam2bcf.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bam2bcf_edlib.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bam_sample.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bcftools.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/bin.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/ccall.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/cols.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm6 4-cpython-311/bcftools/consensus.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/convert.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/csq.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/dist.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/edlib.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/em.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/extsort.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/filter.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/gff.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/gvcf.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/hclust.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/kmin.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/main.c.pysam.o build/temp.free bsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/mcall.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/mpileup.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/ploidy.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/prob1.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/read_consensus.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/regidx.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/reheader.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/smpl_ilist.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/str_finder.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/tabix.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/tsv2vcf.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfannotate.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8 -arm64-cpython-311/bcftools/vcfbuf.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfcall.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfcnv.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfconcat.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfconvert.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcffilter.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfgtcheck.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfhead.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfindex.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfisec.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfmerge.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfnorm.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/ bcftools/vcfplugin.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfquery.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfroh.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfsom.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfsort.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfstats.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcfview.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/vcmp.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/bcftools/version.c.pysam.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcbcftools.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cp ython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -o build/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcbcftools.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcutils.pyx because it changed. [1/1] Cythonizing pysam/libcutils.pyx building 'pysam.libcutils' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libcutils.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/pysam_util.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcutils.o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/pysam_util.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcsamtools.cpython-311 -lcbcftools.cpython-311 -o build/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcutils.cpython-311.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignmentfile.pyx:2567:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2572:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2577:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2616:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2621:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2626:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation Compiling pysam/libcalignmentfile.pyx because it changed. [1/1] Cythonizing pysam/libcalignmentfile.pyx building 'pysam.libcalignmentfile' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libcalignmentfile.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcalignmentfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcalignmentfile.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcsamfile.pyx because it changed. [1/1] Cythonizing pysam/libcsamfile.pyx building 'pysam.libcsamfile' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libcsamfile.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcsamfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcsamfile.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcalignedsegment.pyx because it changed. [1/1] Cythonizing pysam/libcalignedsegment.pyx building 'pysam.libcalignedsegment' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libcalignedsegment.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcalignedsegment.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcalignedsegment.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabix.pyx because it changed. [1/1] Cythonizing pysam/libctabix.pyx building 'pysam.libctabix' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libctabix.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libctabix.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libctabix.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcfaidx.pyx because it changed. [1/1] Cythonizing pysam/libcfaidx.pyx building 'pysam.libcfaidx' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libcfaidx.c -o build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcfaidx.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -Lbuild/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-14.3-RELEASE-p8-arm64-cpython-311/pysam/libcfaidx.cpython-311.so -Wl,-rpath,$ORIGIN Fatal error 'PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace. mutex 0x316dd2e43788 own 0xbf192 is on list 0x316dd2e469b0 0x0' at line 151 in file /usr/src/lib/libthr/thread/thr_mutex.c (errno = 0) cc: error: unable to execute command: Abort trap (core dumped) cc: error: linker command failed due to signal (use -v to see invocation) error: command '/usr/bin/cc' failed with exit code 1 *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-pysam
