=>> Building biology/py-pysam build started at Fri Jan 23 09:10:05 EST 2026 port directory: /usr/ports/biology/py-pysam package name: py311-pysam-0.23.0_1 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1128 Jun 29 2025 /usr/ports/biology/py-pysam/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: 4f0eba1efd73 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 09 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/09/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py311 MAKE_ARGS= FLAVOR=py311 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --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=freebsd13 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=13.5 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=freebsd13 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--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> 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 [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] 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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-pysam-0.23.0_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by 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. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py311-pysam-0.23.0_1 =========================================================================== =================================================== ===== 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 [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> 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 [pkg.DaveG.ca] Installing py311-cython-3.2.4... [pkg.DaveG.ca] `-- Installing python311-3.11.14... [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] Extracting py311-cython-3.2.4: .......... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> py311-pysam-0.23.0_1 depends on package: py311-cython>=3.2.4 - found ===> Returning to build of py311-pysam-0.23.0_1 ===> py311-pysam-0.23.0_1 depends on package: py311-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py311-setuptools-63.1.0_3.pkg [pkg.DaveG.ca] Installing py311-setuptools-63.1.0_3... [pkg.DaveG.ca] Extracting py311-setuptools-63.1.0_3: .......... done ===> py311-pysam-0.23.0_1 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-pysam-0.23.0_1 ===> py311-pysam-0.23.0_1 depends on file: /usr/local/bin/python3.11 - found ===> py311-pysam-0.23.0_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> py311-pysam-0.23.0_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-pysam-0.23.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pysam-0.23.0_1 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.22.pkg [pkg.DaveG.ca] Installing htslib-1.22... [pkg.DaveG.ca] `-- Installing curl-8.17.0... [pkg.DaveG.ca] | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing libunistring-1.4.1... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.4.1: .......... done [pkg.DaveG.ca] | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] `-- Extracting curl-8.17.0: .......... done [pkg.DaveG.ca] `-- Installing libdeflate-1.25... [pkg.DaveG.ca] `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] Extracting htslib-1.22: .......... done ===> py311-pysam-0.23.0_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of py311-pysam-0.23.0_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py311-pysam-0.23.0_1 # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py311-pysam-0.23.0_1 # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating build creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311 creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/Pileup.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/version.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/config.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/utils.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/bcftools.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/samtools.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include copying pysam/include/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'pysam/libc*.c' no previously-included directories found matching 'tests/' warning: no previously-included files found matching 'htslib/*config*.h' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pysam.include.samtools.lz4' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pysam.include.samtools.lz4' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pysam.include.samtools.lz4' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying pysam/cbcftools_util.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/csamtools_util.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/htslib_util.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/htslib_util.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcalignedsegment.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcalignedsegment.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcalignedsegment.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcalignmentfile.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcalignmentfile.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcalignmentfile.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbcf.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbcf.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbcf.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbcftools.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbcftools.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbcftools.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbgzf.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbgzf.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbgzf.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcfaidx.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcfaidx.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcfaidx.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libchtslib.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libchtslib.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libchtslib.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcsamfile.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcsamfile.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcsamfile.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcsamtools.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcsamtools.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcsamtools.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libctabix.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libctabix.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libctabix.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libctabixproxies.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libctabixproxies.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libctabixproxies.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcutils.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcutils.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcutils.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcvcf.pxd -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcvcf.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcvcf.pyx -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/py.typed -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/pysam_stream.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/pysam_util.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/pysam_util.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/version.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/version.pyi -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/LICENSE -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/README -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_color.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_import.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_index.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_md.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_split.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bamtk.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bedcov.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bedidx.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/bedidx.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/coverage.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/cram_size.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/cut_target.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/dict.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/faidx.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/padding.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/phase.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/reference.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/reset.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/sam_view.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/sample.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/sample.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/samtools.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/splaysort.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/stats.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools copying samtools/version.sh -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/README -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_edlib.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_edlib.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bin.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/bin.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/call.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/cols.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/cols.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/convert.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/convert.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/csq.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/dist.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/dist.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/edlib.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/edlib.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/edlib.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/em.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/filter.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/filter.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/gff.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/gff.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/hex.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/main.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/mw.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/version.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/version.sh -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools copying bcftools/config.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools running build_ext Compiling pysam/libchtslib.pyx because it changed. [1/1] Cythonizing pysam/libchtslib.pyx building 'pysam.libchtslib' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311 creating build/temp.freebsd-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/pysam/htslib_util.o build/temp.freebsd-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -o build/lib.freebsd-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/samtools creating build/temp.freebsd-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamtools.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/amplicon_stats.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam2depth.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_addrprg.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_ampliconclip.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_aux.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_cat.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_color.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_consensus.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_fastq.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_flags.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_import.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_index.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_lpileup.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_markdup.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_mate.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_md.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_plbuf.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_plcmd.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_quickcheck.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_reheader.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_rmdup.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_rmdupse.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_samples.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_sort.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_split.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bam_stat.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bamshuf.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bamtk.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bedcov.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/bedidx.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/consensus_pileup.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/coverage.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/cram_size.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/cut_target.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/dict.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/faidx.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/lz4/lz4.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/padding.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/phase.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/reference.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/reset.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/sam_opts.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/sam_utils.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/sam_view.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/sample.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/samtools.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/stats.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/samtools/stats_isize.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/bcftools/HMM.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/abuf.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/bam2bcf.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/bam2bcf_edlib.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/bam_sample.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/bcftools.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/bin.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/ccall.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/cols.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/consensus.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/convert.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/csq.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/dist.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/edlib.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/em.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/extsort.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/filter.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/gff.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/gvcf.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/hclust.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/kmin.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/main.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/mcall.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/mpileup.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/ploidy.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/prob1.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/read_consensus.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/regidx.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/reheader.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/smpl_ilist.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/str_finder.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/tabix.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/tsv2vcf.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfannotate.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfbuf.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfcall.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfcnv.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfconcat.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfconvert.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcffilter.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfgtcheck.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfhead.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfindex.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfisec.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfmerge.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfnorm.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfplugin.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfquery.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfroh.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfsom.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfsort.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfstats.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcfview.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/vcmp.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bcftools/version.c.pysam.o build/temp.freebsd-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcutils.o build/temp.freebsd-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcsamtools.cpython-311 -lcbcftools.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignmentfile.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcsamfile.pyx because it changed. [1/1] Cythonizing pysam/libcsamfile.pyx building 'pysam.libcsamfile' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libcsamfile.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamfile.cpython-311.so -Wl,-rpath,$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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignedsegment.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabix.pyx because it changed. [1/1] Cythonizing pysam/libctabix.pyx building 'pysam.libctabix' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libctabix.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabix.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabix.cpython-311.so -Wl,-rpath,$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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-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-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcfaidx.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcf.pyx because it changed. [1/1] Cythonizing pysam/libcbcf.pyx building 'pysam.libcbcf' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0 -I/usr/local/include/python3.11 -c pysam/libcbcf.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcf.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbgzf.pyx because it changed. [1/1] Cythonizing pysam/libcbgzf.pyx building 'pysam.libcbgzf' 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/libcbgzf.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbgzf.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-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbgzf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbgzf.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabixproxies.pyx because it changed. [1/1] Cythonizing pysam/libctabixproxies.pyx building 'pysam.libctabixproxies' 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/libctabixproxies.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabixproxies.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-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabixproxies.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabixproxies.cpython-311.so -Wl,-rpath,$ORIGIN warning: pysam/libcvcf.pyx:1083:27: Unreachable code Compiling pysam/libcvcf.pyx because it changed. [1/1] Cythonizing pysam/libcvcf.pyx building 'pysam.libcvcf' 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/libcvcf.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcvcf.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-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcvcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.23.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -Lbuild/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcvcf.cpython-311.so -Wl,-rpath,$ORIGIN =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pysam-0.23.0_1 depends on executable: bcftools - not found ===> Installing existing package /packages/All/bcftools-1.22.pkg [pkg.DaveG.ca] Installing bcftools-1.22... [pkg.DaveG.ca] `-- Installing bash-5.3.9... [pkg.DaveG.ca] `-- Extracting bash-5.3.9: .......... done [pkg.DaveG.ca] `-- Installing gsl-2.7.1_1... [pkg.DaveG.ca] `-- Extracting gsl-2.7.1_1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting bcftools-1.22: .......... done ===> py311-pysam-0.23.0_1 depends on executable: bcftools - found ===> Returning to build of py311-pysam-0.23.0_1 ===> py311-pysam-0.23.0_1 depends on executable: samtools - not found ===> Installing existing package /packages/All/samtools-1.22.pkg [pkg.DaveG.ca] Installing samtools-1.22... [pkg.DaveG.ca] Extracting samtools-1.22: .......... done ===> py311-pysam-0.23.0_1 depends on executable: samtools - 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 - found ===> py311-pysam-0.23.0_1 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py311-pysam-0.23.0_1 ===> Generating temporary packing list # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install /usr/local/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py copying pysam/config.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' warning: no previously-included files found matching 'htslib/*config*.h' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pysam.include.samtools.lz4' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pysam.include.samtools.lz4' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pysam.include.samtools.lz4' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying pysam/libcalignedsegment.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcalignmentfile.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbcf.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbcftools.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcbgzf.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcfaidx.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libchtslib.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcsamfile.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcsamtools.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libctabix.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libctabixproxies.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcutils.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying pysam/libcvcf.c -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam copying samtools/samtools_config_vars.h -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools running build_ext creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension running install_lib creating /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11 creating /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/Pileup.py -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam creating /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/__init__.py -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include creating /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfconvert.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/reheader.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfsort.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/tabix.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcmp.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcmp.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam2bcf.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam2bcf.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/edlib.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/regidx.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/version.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/edlib.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/edlib.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/kmin.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/prob1.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/prob1.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/extsort.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/extsort.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfcnv.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/smpl_ilist.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/smpl_ilist.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/variantkey.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfcnv.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/reheader.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfsom.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfindex.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfisec.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfindex.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfstats.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/regidx.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/regidx.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/convert.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/convert.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/abuf.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/abuf.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfplugin.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/hclust.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/hclust.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/abuf.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfannotate.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfhead.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/consensus.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/HMM.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/cigar_state.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bcftools.pysam.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bcftools.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/ploidy.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/ploidy.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/read_consensus.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/read_consensus.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/mpileup.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/read_consensus.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfconcat.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/mcall.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfisec.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/ccall.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/version.sh -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfconcat.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfcall.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfroh.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfsort.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/em.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcffilter.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfnorm.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/version.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/em.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/filter.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfquery.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam2bcf.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/csq.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/prob1.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/ccall.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/filter.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/filter.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfplugin.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfmerge.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/utlist.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/gff.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/gff.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam_sample.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam_sample.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/dbuf.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfbuf.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfhead.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam_sample.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bin.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bin.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfsom.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/LICENSE -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/main.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/khash_str2str.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam2bcf_indel.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bcftools.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/ploidy.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/config.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam2bcf_edlib.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/main.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/call.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/rbuf.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bin.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/csq.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/dist.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/hex.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcmp.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfroh.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfgtcheck.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/mcall.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/cols.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/cols.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/README -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/kmin.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/kmin.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/convert.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfannotate.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/tsv2vcf.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/tsv2vcf.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/str_finder.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/str_finder.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/HMM.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/HMM.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/mpileup.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcffilter.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/gvcf.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/gvcf.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/dist.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/dist.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/gvcf.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfview.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfnorm.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfmerge.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/cols.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/hclust.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/consensus.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfconvert.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfstats.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfview.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfquery.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/str_finder.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfbuf.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfbuf.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/vcfcall.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/bam2bcf_edlib.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/kheap.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/gff.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/extsort.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/tabix.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/bcftools/mw.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools creating /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_stat.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/sam_view.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/tmp_file.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_markdup.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_color.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_aux.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bamshuf.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/amplicon_stats.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_split.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_lpileup.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_lpileup.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_mate.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_addrprg.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_flags.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/coverage.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_samples.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_stat.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_plbuf.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_plbuf.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_rmdup.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_samples.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_ampliconclip.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_ampliconclip.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/cut_target.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/stats.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_fastq.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_md.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_reheader.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/sam_opts.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/sam_view.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/padding.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_plcmd.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/version.sh -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_split.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/consensus_pileup.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/faidx.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bamtk.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/stats_isize.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/stats_isize.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bedidx.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/coverage.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_color.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_quickcheck.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/stats_isize.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/consensus_pileup.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/consensus_pileup.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_cat.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/reset.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/reference.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_md.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/reference.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam2depth.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_markdup.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_sort.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_lpileup.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_rmdup.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/dict.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/LICENSE -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/splaysort.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bedcov.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/dict.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/stats.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/tmp_file.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/tmp_file.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/sam_utils.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/sam_utils.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_consensus.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/config.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_addrprg.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/sam_opts.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/sam_opts.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/sample.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/sample.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bamtk.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/padding.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_cat.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/faidx.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/phase.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_index.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/phase.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/README -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_aux.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/sample.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_flags.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/samtools.pysam.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/samtools.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_import.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_plbuf.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam2depth.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/samtools_config_vars.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_rmdupse.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/amplicon_stats.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_consensus.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/cram_size.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bedcov.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools creating /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools/lz4 copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/lz4/lz4.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools/lz4 copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/lz4/lz4.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools/lz4 copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/lz4/LICENSE -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools/lz4 copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/lz4/lz4.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools/lz4 copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/cut_target.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_plcmd.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_sort.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_fastq.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bamshuf.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/sam_utils.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/cram_size.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_import.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_mate.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_index.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bam_reheader.c.pysam.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bedidx.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/bedidx.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/reset.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/include/samtools/samtools.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignedsegment.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/version.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcftools.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabixproxies.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcutils.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcutils.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcfaidx.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcutils.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignmentfile.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignmentfile.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignmentfile.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbgzf.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcfaidx.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabix.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbgzf.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbgzf.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcfaidx.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcfaidx.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignedsegment.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/__init__.py -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignedsegment.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignedsegment.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignedsegment.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/version.py -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamtools.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignmentfile.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcfaidx.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbgzf.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcvcf.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamfile.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamfile.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamfile.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcutils.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/version.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabixproxies.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcvcf.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcf.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcf.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libchtslib.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamfile.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcf.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/pysam_stream.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcvcf.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcvcf.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabix.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/csamtools_util.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcvcf.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/pysam_util.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/pysam_util.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libchtslib.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamtools.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/config.py -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcftools.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcftools.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcftools.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcalignmentfile.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabix.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamfile.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcf.cpython-311.so -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/py.typed -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabix.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabix.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/utils.py -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/cbcftools_util.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/bcftools.py -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcftools.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcutils.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbcf.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamtools.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamtools.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcsamtools.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/htslib_util.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/htslib_util.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/samtools.py -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabixproxies.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabixproxies.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libctabixproxies.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libchtslib.pyx -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libchtslib.pyi -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libchtslib.pxd -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/pysam/libcbgzf.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam byte-compiling /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/Pileup.py to Pileup.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/version.py to version.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/config.py to config.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/utils.py to utils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/bcftools.py to bcftools.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/samtools.py to samtools.cpython-311.pyc writing byte-compilation script '/tmp/tmpd0w53_59.py' /usr/local/bin/python3.11 /tmp/tmpd0w53_59.py removing /tmp/tmpd0w53_59.py running install_egg_info Copying pysam.egg-info to /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam-0.23.0-py3.11.egg-info running install_scripts writing list of installed files to '/wrkdirs/usr/ports/biology/py-pysam/work-py311/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-01-23T14:10:05+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=4f0eba1efd73' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for py311-pysam-0.23.0_1 ===> Building py311-pysam-0.23.0_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-pysam-0.23.0_1 build of biology/py-pysam@py311 | py311-pysam-0.23.0_1 ended at Fri Jan 23 09:15:51 EST 2026 build time: 00:05:48