=>> Building biology/py-pysam build started at Fri May 29 14:40:36 JST 2026 port directory: /usr/ports/biology/py-pysam package name: py311-pysam-0.24.0 building for: FreeBSD curamd64-setuptools-job-02 16.0-CURRENT FreeBSD 16.0-CURRENT 1600018 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1191 May 2 10:17 /usr/ports/biology/py-pysam/Makefile Ports top last git commit: a8b187544 Ports top unclean checkout: yes Port dir last git commit: a8b187544 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4 Host OSVERSION: 1600018 Jail OSVERSION: 1600018 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600018 UNAME_v=FreeBSD 16.0-CURRENT 1600018 UNAME_r=16.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.4 MASTERMNT=/usr/local/poudriere/data/.m/curamd64-setuptools/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/usr/local/poudriere/data/.m/curamd64-setuptools/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=curamd64-setuptools SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/curamd64-setuptools/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4 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=freebsd16 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=16.0 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=freebsd16 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+= magick=7-x11 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5_mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= GAMMA INPUTMETHOD LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif 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+= magick=7-x11 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5_mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= GAMMA INPUTMETHOD LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif #### Misc Poudriere #### .include "/etc/make.conf.ports_env" DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 12099 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License MIT accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pysam-0.24.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [curamd64-setuptools-job-02] Installing pkg-2.7.5... [curamd64-setuptools-job-02] Extracting pkg-2.7.5: .......... done ===> py311-pysam-0.24.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-pysam-0.24.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user => pysam-developers-pysam-v0.24.0_GH0.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://codeload.github.com/pysam-developers/pysam/tar.gz/v0.24.0?dummy=/pysam-developers-pysam-v0.24.0_GH0.tar.gz fetch: https://codeload.github.com/pysam-developers/pysam/tar.gz/v0.24.0?dummy=/pysam-developers-pysam-v0.24.0_GH0.tar.gz: size unknown fetch: https://codeload.github.com/pysam-developers/pysam/tar.gz/v0.24.0?dummy=/pysam-developers-pysam-v0.24.0_GH0.tar.gz: size of remote file is not known pysam-developers-pysam-v0.24.0_GH0.tar.gz 4099 kB 7193 kBps 00s ===> Fetching all distfiles required by py311-pysam-0.24.0 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by py311-pysam-0.24.0 for building => SHA256 Checksum OK for pysam-developers-pysam-v0.24.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License MIT accepted by the user ===> Fetching all distfiles required by py311-pysam-0.24.0 for building ===> Extracting for py311-pysam-0.24.0 => SHA256 Checksum OK for pysam-developers-pysam-v0.24.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for py311-pysam-0.24.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pysam-0.24.0 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [curamd64-setuptools-job-02] Installing gmake-4.4.1... [curamd64-setuptools-job-02] `-- Installing gettext-runtime-1.0... [curamd64-setuptools-job-02] | `-- Installing indexinfo-0.3.1_1... [curamd64-setuptools-job-02] | `-- Extracting indexinfo-0.3.1_1: .... done [curamd64-setuptools-job-02] `-- Extracting gettext-runtime-1.0: .......... done [curamd64-setuptools-job-02] Extracting gmake-4.4.1: .......... done ===> py311-pysam-0.24.0 depends on package: gmake>=4.4.1 - found ===> Returning to build of py311-pysam-0.24.0 ===> py311-pysam-0.24.0 depends on package: py311-cython>=3.2.4 - not found ===> Installing existing package /packages/All/py311-cython-3.2.4.pkg [curamd64-setuptools-job-02] Installing py311-cython-3.2.4... [curamd64-setuptools-job-02] `-- Installing python311-3.11.15_2... [curamd64-setuptools-job-02] | `-- Installing libffi-3.5.1... [curamd64-setuptools-job-02] | `-- Extracting libffi-3.5.1: .......... done [curamd64-setuptools-job-02] | `-- Installing mpdecimal-4.0.1... [curamd64-setuptools-job-02] | `-- Extracting mpdecimal-4.0.1: .......... done [curamd64-setuptools-job-02] | `-- Installing openssl-3.0.20,1... [curamd64-setuptools-job-02] | `-- Extracting openssl-3.0.20,1: .......... done [curamd64-setuptools-job-02] | `-- Installing readline-8.3.3... [curamd64-setuptools-job-02] | `-- Extracting readline-8.3.3: .......... done [curamd64-setuptools-job-02] `-- Extracting python311-3.11.15_2: .......... done [curamd64-setuptools-job-02] Extracting py311-cython-3.2.4: .......... done ===== Message from python311-3.11.15_2: -- 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-0.24.0 depends on package: py311-cython>=3.2.4 - found ===> Returning to build of py311-pysam-0.24.0 ===> py311-pysam-0.24.0 depends on package: py311-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py311-setuptools-81.0.0.pkg [curamd64-setuptools-job-02] Installing py311-setuptools-81.0.0... [curamd64-setuptools-job-02] `-- Installing py311-more-itertools-10.6.0... [curamd64-setuptools-job-02] `-- Extracting py311-more-itertools-10.6.0: .......... done [curamd64-setuptools-job-02] `-- Installing py311-packaging-26.2... [curamd64-setuptools-job-02] `-- Extracting py311-packaging-26.2: .......... done [curamd64-setuptools-job-02] `-- Installing py311-wheel-0.47.0... [curamd64-setuptools-job-02] `-- Extracting py311-wheel-0.47.0: .......... done [curamd64-setuptools-job-02] Extracting py311-setuptools-81.0.0: .......... done ===> py311-pysam-0.24.0 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-pysam-0.24.0 ===> py311-pysam-0.24.0 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pysam-0.24.0 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.23.1.pkg [curamd64-setuptools-job-02] Installing htslib-1.23.1... [curamd64-setuptools-job-02] `-- Installing curl-8.19.0_2... [curamd64-setuptools-job-02] | `-- Installing brotli-1.2.0,1... [curamd64-setuptools-job-02] | `-- Extracting brotli-1.2.0,1: .......... done [curamd64-setuptools-job-02] | `-- Installing libidn2-2.3.8... [curamd64-setuptools-job-02] | | `-- Installing libunistring-1.4.2... [curamd64-setuptools-job-02] | | `-- Extracting libunistring-1.4.2: .......... done [curamd64-setuptools-job-02] | `-- Extracting libidn2-2.3.8: .......... done [curamd64-setuptools-job-02] | `-- Installing libnghttp2-1.69.0... [curamd64-setuptools-job-02] | `-- Extracting libnghttp2-1.69.0: .......... done [curamd64-setuptools-job-02] | `-- Installing libpsl-0.21.5_2... [curamd64-setuptools-job-02] | `-- Extracting libpsl-0.21.5_2: .......... done [curamd64-setuptools-job-02] | `-- Installing libssh2-1.11.1,3... [curamd64-setuptools-job-02] | `-- Extracting libssh2-1.11.1,3: .......... done [curamd64-setuptools-job-02] | `-- Installing zstd-1.5.7_1... [curamd64-setuptools-job-02] | `-- Extracting zstd-1.5.7_1: .......... done [curamd64-setuptools-job-02] `-- Extracting curl-8.19.0_2: .......... done [curamd64-setuptools-job-02] `-- Installing libdeflate-1.25... [curamd64-setuptools-job-02] `-- Extracting libdeflate-1.25: .......... done [curamd64-setuptools-job-02] Extracting htslib-1.23.1: .......... done ===> py311-pysam-0.24.0 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of py311-pysam-0.24.0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for py311-pysam-0.24.0 /usr/local/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) # pysam: Cython 3.2.4 is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for py311-pysam-0.24.0 /usr/local/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) # pysam: Cython 3.2.4 is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/Pileup.py -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/__init__.py -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/bcftools.py -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/samtools.py -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/utils.py -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/version.py -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/config.py -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam creating build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include copying pysam/include/__init__.py -> build/lib.freebsd-16.0-CURRENT-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' 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 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/conftest_cstd.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/htslib_util.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/htslib_util.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcalignedsegment.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcalignedsegment.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcalignedsegment.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcalignmentfile.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcalignmentfile.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcalignmentfile.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbcf.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbcf.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbcf.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbcftools.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbcftools.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbcftools.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbgzf.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbgzf.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbgzf.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcfaidx.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcfaidx.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcfaidx.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libchtslib.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libchtslib.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libchtslib.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcsamfile.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcsamfile.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcsamfile.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcsamtools.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcsamtools.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcsamtools.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libctabix.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libctabix.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libctabix.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libctabixproxies.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libctabixproxies.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libctabixproxies.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcutils.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcutils.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcutils.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcvcf.pxd -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcvcf.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcvcf.pyx -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/py.typed -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/version.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/version.pyi -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam creating build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/LICENSE -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/README -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_checksum.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_checksum.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_color.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_consensus_tab.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_import.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_index.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_md.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_split.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bamtk.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bedcov.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bedidx.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/bedidx.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/coverage.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/cram_size.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/cut_target.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/dict.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/faidx.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/padding.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/phase.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/reference.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/reset.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/sam_view.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/sample.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/sample.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/samtools.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/splaysort.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/stats.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/version.sh -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools creating build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools creating build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/README -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_edlib.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_edlib.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bin.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/bin.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/call.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/cols.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/cols.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/convert.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/convert.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/csq.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/dist.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/dist.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/edlib.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/edlib.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/edlib.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/em.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/filter.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/filter.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/gff.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/gff.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/hex.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/main.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/mw.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/version.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/version.sh -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools copying bcftools/config.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools running build_ext checking for cc option to enable C99 features... creating build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c pysam/conftest_cstd.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/conftest_cstd.o cc option to enable C99 features: none needed Compiling pysam/libchtslib.pyx because it changed. [1/1] Cythonizing pysam/libchtslib.pyx building 'pysam.libchtslib' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/htslib_util.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libchtslib.c -o build/temp.freebsd-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/htslib_util.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libchtslib.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -o build/lib.freebsd-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/samtools creating build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/lz4 cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libcsamtools.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/amplicon_stats.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam2depth.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_addrprg.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_aux.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_cat.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_checksum.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_checksum.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_color.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_consensus.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_fastq.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_flags.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_import.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_index.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_lpileup.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_markdup.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_mate.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_md.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_plbuf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_plcmd.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_reheader.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_rmdup.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_samples.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_sort.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_split.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bam_stat.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bamshuf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bamtk.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bedcov.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/bedidx.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/consensus_pileup.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/coverage.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/cram_size.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/cut_target.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/dict.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/faidx.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/lz4/lz4.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/padding.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/phase.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/reference.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/reset.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/sam_opts.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/sam_utils.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/sam_view.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/sample.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/samtools.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/stats.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/stats_isize.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c samtools/tmp_file.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/libcsamtools.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/amplicon_stats.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam2depth.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_addrprg.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_ampliconclip.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_aux.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_cat.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_checksum.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_color.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_consensus.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_fastq.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_flags.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_import.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_index.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_lpileup.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_markdup.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_mate.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_md.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_plbuf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_plcmd.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_quickcheck.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_reheader.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_rmdup.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_rmdupse.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_samples.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_sort.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_split.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bam_stat.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bamshuf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bamtk.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bedcov.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/bedidx.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/consensus_pileup.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/coverage.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/cram_size.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/cut_target.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/dict.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/faidx.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/lz4/lz4.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/padding.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/phase.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/reference.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/reset.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/sam_opts.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/sam_utils.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/sam_view.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/sample.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/samtools.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/stats.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/stats_isize.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/samtools/tmp_file.c.pysam.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -o build/lib.freebsd-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/bcftools cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/HMM.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/abuf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/bam2bcf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/bam2bcf_edlib.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bam2bcf_edlib.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/bam_sample.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/bcftools.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/bin.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/ccall.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/cols.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/consensus.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/convert.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/csq.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/dist.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/edlib.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/edlib.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/em.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/extsort.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/filter.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/gff.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/gff.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/gvcf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/hclust.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/kmin.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/main.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/mcall.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/mpileup.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/ploidy.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/prob1.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/read_consensus.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/regidx.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/reheader.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/str_finder.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/tabix.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfannotate.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfbuf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfcall.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfcnv.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfconcat.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfconvert.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcffilter.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfhead.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfindex.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfisec.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfmerge.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfnorm.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfplugin.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfquery.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfroh.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfsom.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfsort.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfstats.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcfview.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/vcmp.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c bcftools/version.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libcbcftools.c -o build/temp.freebsd-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/bcftools/HMM.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/abuf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bam2bcf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bam2bcf_edlib.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bam_sample.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bcftools.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/bin.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/ccall.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/cols.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/consensus.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/convert.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/csq.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/dist.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/edlib.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/em.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/extsort.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/filter.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/gff.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/gvcf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/hclust.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/kmin.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/main.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/mcall.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/mpileup.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/ploidy.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/prob1.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/read_consensus.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/regidx.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/reheader.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/smpl_ilist.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/str_finder.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/tabix.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/tsv2vcf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfannotate.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfbuf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfcall.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfcnv.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfconcat.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfconvert.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcffilter.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfgtcheck.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfhead.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfindex.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfisec.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfmerge.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfnorm.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfplugin.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfquery.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfroh.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfsom.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfsort.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfstats.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcfview.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/vcmp.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/bcftools/version.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcbcftools.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -o build/lib.freebsd-16.0-CURRENT-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libcutils.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcutils.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-16.0-CURRENT-amd64-cpython-311/pysam/libcutils.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcsamtools.cpython-311 -lcbcftools.cpython-311 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcutils.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcalignmentfile.pyx because it changed. [1/1] Cythonizing pysam/libcalignmentfile.pyx building 'pysam.libcalignmentfile' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libcalignmentfile.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcalignmentfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcalignmentfile.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcsamfile.pyx because it changed. [1/1] Cythonizing pysam/libcsamfile.pyx building 'pysam.libcsamfile' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libcsamfile.c -o build/temp.freebsd-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/libcsamfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcsamfile.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcalignedsegment.pyx because it changed. [1/1] Cythonizing pysam/libcalignedsegment.pyx building 'pysam.libcalignedsegment' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libcalignedsegment.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcalignedsegment.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcalignedsegment.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabix.pyx because it changed. [1/1] Cythonizing pysam/libctabix.pyx building 'pysam.libctabix' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libctabix.c -o build/temp.freebsd-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/libctabix.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libctabix.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcfaidx.pyx because it changed. [1/1] Cythonizing pysam/libcfaidx.pyx building 'pysam.libcfaidx' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libcfaidx.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcfaidx.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcfaidx.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcf.pyx because it changed. [1/1] Cythonizing pysam/libcbcf.pyx building 'pysam.libcbcf' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libcbcf.c -o build/temp.freebsd-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/libcbcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcbcf.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbgzf.pyx because it changed. [1/1] Cythonizing pysam/libcbgzf.pyx building 'pysam.libcbgzf' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libcbgzf.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcbgzf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcbgzf.cpython-311.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabixproxies.pyx because it changed. [1/1] Cythonizing pysam/libctabixproxies.pyx building 'pysam.libctabixproxies' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libctabixproxies.c -o build/temp.freebsd-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/libctabixproxies.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libctabixproxies.cpython-311.so -Wl,-rpath,$ORIGIN warning: pysam/libcvcf.pyx:1084:27: Unreachable code Compiling pysam/libcvcf.pyx because it changed. [1/1] Cythonizing pysam/libcvcf.pyx building 'pysam.libcvcf' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0 -I/usr/local/include/python3.11 -c pysam/libcvcf.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcvcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py311/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-311 -lcutils.cpython-311 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/libcvcf.cpython-311.so -Wl,-rpath,$ORIGIN =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pysam-0.24.0 depends on executable: bcftools - not found ===> Installing existing package /packages/All/bcftools-1.23.1.pkg [curamd64-setuptools-job-02] Installing bcftools-1.23.1... [curamd64-setuptools-job-02] `-- Installing bash-5.3.9... [curamd64-setuptools-job-02] `-- Extracting bash-5.3.9: .......... done [curamd64-setuptools-job-02] `-- Installing gsl-2.8... [curamd64-setuptools-job-02] `-- Extracting gsl-2.8: .......... done [curamd64-setuptools-job-02] `-- Installing perl5-5.42.2... [curamd64-setuptools-job-02] `-- Extracting perl5-5.42.2: .......... done [curamd64-setuptools-job-02] Extracting bcftools-1.23.1: .......... done ===> py311-pysam-0.24.0 depends on executable: bcftools - found ===> Returning to build of py311-pysam-0.24.0 ===> py311-pysam-0.24.0 depends on executable: samtools - not found ===> Installing existing package /packages/All/samtools-1.23.1.pkg [curamd64-setuptools-job-02] Installing samtools-1.23.1... [curamd64-setuptools-job-02] Extracting samtools-1.23.1: .......... done ===> py311-pysam-0.24.0 depends on executable: samtools - found ===> Returning to build of py311-pysam-0.24.0 ===> py311-pysam-0.24.0 depends on package: py311-cython>=3.2.4 - found ===> py311-pysam-0.24.0 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for py311-pysam-0.24.0 ===> Generating temporary packing list /usr/local/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) # pysam: Cython 3.2.4 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/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying pysam/config.py -> build/lib.freebsd-16.0-CURRENT-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' 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 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/libcalignedsegment.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcalignmentfile.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbcf.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbcftools.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcbgzf.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcfaidx.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libchtslib.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcsamfile.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcsamtools.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libctabix.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libctabixproxies.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcutils.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying pysam/libcvcf.c -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam copying samtools/config.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying samtools/samtools_config_vars.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools copying bcftools/config.h -> build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/include/bcftools running build_ext checking for cc option to enable C99 features... cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c pysam/conftest_cstd.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/conftest_cstd.o cc option to enable C99 features: none needed 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/site-packages creating /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-16.0-CURRENT-amd64-cpython-311/pysam/Pileup.py -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/config.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-16.0-CURRENT-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/samtools copying build/lib.freebsd-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools/bam_checksum.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools/bam_checksum.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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/include/samtools/bam_consensus_tab.h -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.freebsd-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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 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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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 copying build/lib.freebsd-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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 creating /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.freebsd-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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 copying build/lib.freebsd-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/conftest_cstd.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/libcbgzf.c -> /wrkdirs/usr/ports/biology/py-pysam/work-py311/stage/usr/local/lib/python3.11/site-packages/pysam copying build/lib.freebsd-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-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-16.0-CURRENT-amd64-cpython-311/pysam/libcvcf.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/__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/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 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/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/include/__init__.py to __init__.cpython-311.pyc writing byte-compilation script '/tmp/tmpa61tqjxx.py' /usr/local/bin/python3.11 /tmp/tmpa61tqjxx.py removing /tmp/tmpa61tqjxx.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-0.24.0-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=2026-05-29T05:40:36+0000' 'PKG_NOTE_ports_top_git_hash=a8b187544' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=a8b187544' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.4' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for py311-pysam-0.24.0 ===> Building py311-pysam-0.24.0 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-pysam-0.24.0 build of biology/py-pysam@py311 | py311-pysam-0.24.0 ended at Fri May 29 14:49:39 JST 2026 build time: 00:11:41