=>> Building biology/py-bx-python build started at Fri Jan 23 10:37:00 EST 2026 port directory: /usr/ports/biology/py-bx-python package name: py311-bx-python-0.14.0 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 930 Jan 15 19:47 /usr/ports/biology/py-bx-python/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: 6d475ab2dcd0 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 10 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/10/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py311 MAKE_ARGS= FLAVOR=py311 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-bx-python/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-bx-python/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-bx-python/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-bx-python/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bx-python" EXAMPLESDIR="share/examples/bx-python" DATADIR="share/bx-python" WWWDIR="www/bx-python" ETCDIR="etc/bx-python" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bx-python DOCSDIR=/usr/local/share/doc/bx-python EXAMPLESDIR=/usr/local/share/examples/bx-python WWWDIR=/usr/local/www/bx-python ETCDIR=/usr/local/etc/bx-python --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-bx-python-0.14.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> py311-bx-python-0.14.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-bx-python-0.14.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-bx-python-0.14.0 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-bx-python-0.14.0 for building => SHA256 Checksum OK for bx_python-0.14.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-bx-python-0.14.0 for building ===> Extracting for py311-bx-python-0.14.0 => SHA256 Checksum OK for bx_python-0.14.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py311-bx-python-0.14.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-bx-python-0.14.0 depends on package: py311-setuptools>0 - not found ===> Installing existing package /packages/All/py311-setuptools-63.1.0_3.pkg [pkg.DaveG.ca] Installing py311-setuptools-63.1.0_3... [pkg.DaveG.ca] `-- Installing python311-3.11.14... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] Extracting py311-setuptools-63.1.0_3: .......... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> py311-bx-python-0.14.0 depends on package: py311-setuptools>0 - found ===> Returning to build of py311-bx-python-0.14.0 ===> py311-bx-python-0.14.0 depends on package: py311-numpy>=1.16,1<1.27,1 - not found ===> Installing existing package /packages/All/py311-numpy-1.26.4_12,1.pkg [pkg.DaveG.ca] Installing py311-numpy-1.26.4_12,1... [pkg.DaveG.ca] `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] `-- Extracting gcc14-14.2.0_4: .......... done [pkg.DaveG.ca] `-- Installing openblas-0.3.30,2... [pkg.DaveG.ca] `-- Extracting openblas-0.3.30,2: .......... done [pkg.DaveG.ca] `-- Installing suitesparse-umfpack-6.3.7... [pkg.DaveG.ca] | `-- Installing suitesparse-amd-3.3.4... [pkg.DaveG.ca] | | `-- Installing suitesparse-config-7.12.1... [pkg.DaveG.ca] | | `-- Extracting suitesparse-config-7.12.1: .......... done [pkg.DaveG.ca] | `-- Extracting suitesparse-amd-3.3.4: .......... done [pkg.DaveG.ca] | `-- Installing suitesparse-camd-3.3.5... [pkg.DaveG.ca] | `-- Extracting suitesparse-camd-3.3.5: .......... done [pkg.DaveG.ca] | `-- Installing suitesparse-ccolamd-3.3.5... [pkg.DaveG.ca] | `-- Extracting suitesparse-ccolamd-3.3.5: .......... done [pkg.DaveG.ca] | `-- Installing suitesparse-cholmod-5.3.4... [pkg.DaveG.ca] | | `-- Installing suitesparse-colamd-3.3.5... [pkg.DaveG.ca] | | `-- Extracting suitesparse-colamd-3.3.5: .......... done [pkg.DaveG.ca] | `-- Extracting suitesparse-cholmod-5.3.4: .......... done [pkg.DaveG.ca] `-- Extracting suitesparse-umfpack-6.3.7: .......... done [pkg.DaveG.ca] Extracting py311-numpy-1.26.4_12,1: .......... done ===== Message from gcc14-14.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> py311-bx-python-0.14.0 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> Returning to build of py311-bx-python-0.14.0 ===> py311-bx-python-0.14.0 depends on package: py311-wheel>0 - not found ===> Installing existing package /packages/All/py311-wheel-0.45.1.pkg [pkg.DaveG.ca] Installing py311-wheel-0.45.1... [pkg.DaveG.ca] Extracting py311-wheel-0.45.1: .......... done ===> py311-bx-python-0.14.0 depends on package: py311-wheel>0 - found ===> Returning to build of py311-bx-python-0.14.0 ===> py311-bx-python-0.14.0 depends on package: py311-cython>=3.2.4 - not found ===> Installing existing package /packages/All/py311-cython-3.2.4.pkg [pkg.DaveG.ca] Installing py311-cython-3.2.4... [pkg.DaveG.ca] Extracting py311-cython-3.2.4: .......... done ===> py311-bx-python-0.14.0 depends on package: py311-cython>=3.2.4 - found ===> Returning to build of py311-bx-python-0.14.0 ===> py311-bx-python-0.14.0 depends on file: /usr/local/bin/python3.11 - found ===> py311-bx-python-0.14.0 depends on package: py311-build>=0 - not found ===> Installing existing package /packages/All/py311-build-1.3.0.pkg [pkg.DaveG.ca] Installing py311-build-1.3.0... [pkg.DaveG.ca] `-- Installing py311-packaging-25.0... [pkg.DaveG.ca] `-- Extracting py311-packaging-25.0: .......... done [pkg.DaveG.ca] `-- Installing py311-pyproject-hooks-1.2.0... [pkg.DaveG.ca] `-- Extracting py311-pyproject-hooks-1.2.0: .......... done [pkg.DaveG.ca] Extracting py311-build-1.3.0: .......... done ===> py311-bx-python-0.14.0 depends on package: py311-build>=0 - found ===> Returning to build of py311-bx-python-0.14.0 ===> py311-bx-python-0.14.0 depends on package: py311-installer>=0 - not found ===> Installing existing package /packages/All/py311-installer-0.7.0.pkg [pkg.DaveG.ca] Installing py311-installer-0.7.0... [pkg.DaveG.ca] Extracting py311-installer-0.7.0: .......... done ===> py311-bx-python-0.14.0 depends on package: py311-installer>=0 - found ===> Returning to build of py311-bx-python-0.14.0 ===> py311-bx-python-0.14.0 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc14 create symlink for gcc14 (world) create symlink for g++14 create symlink for g++14 (world) create symlink for cpp14 create symlink for cpp14 (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> py311-bx-python-0.14.0 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-bx-python-0.14.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py311-bx-python-0.14.0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py311-bx-python-0.14.0 * Getting build dependencies for wheel... /usr/local/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py:104: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. warnings.warn(msg, _BetaConfiguration) No parent package detected, impossible to derive `name` running egg_info writing lib/bx_python.egg-info/PKG-INFO writing dependency_links to lib/bx_python.egg-info/dependency_links.txt writing requirements to lib/bx_python.egg-info/requires.txt writing top-level names to lib/bx_python.egg-info/top_level.txt reading manifest file 'lib/bx_python.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'lib/bx_python.egg-info/SOURCES.txt' * Building wheel... /usr/local/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py:104: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. warnings.warn(msg, _BetaConfiguration) No parent package detected, impossible to derive `name` running bdist_wheel running build running build_py creating build creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311 creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras copying lib/bx_extras/fpconst.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras copying lib/bx_extras/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras copying lib/bx_extras/stats.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras copying lib/bx_extras/lrucache.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras copying lib/bx_extras/pstat.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras copying lib/bx_extras/fpconst_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/binned_array.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/bitset_utils.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/binned_array_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/gene_reader.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/bitset_builders.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/filter.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/interval_index_file.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/interval_index_file_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/seqmapping.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/seqmapping_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/wiggle.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/wiggle_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx copying lib/bx/bitset_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi copying lib/bx/bbi/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi copying lib/bx/bbi/bigwig_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif copying lib/bx/motif/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif copying lib/bx/motif/pwm_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif copying lib/bx/motif/pwm.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/seq_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/fasta_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/qdna_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/twobit_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/nib_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/twobit.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/fasta.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/core.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/nib.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/qdna.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq copying lib/bx/seq/seq.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/tabular copying lib/bx/tabular/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/tabular copying lib/bx/tabular/io.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/tabular creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals copying lib/bx/intervals/cluster_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals copying lib/bx/intervals/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals copying lib/bx/intervals/io.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals copying lib/bx/intervals/intersection_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals copying lib/bx/intervals/random_intervals.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intseq copying lib/bx/intseq/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intseq creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align copying lib/bx/align/axt.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align copying lib/bx/align/epo.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align copying lib/bx/align/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align copying lib/bx/align/lav.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align copying lib/bx/align/maf.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align copying lib/bx/align/maf_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align copying lib/bx/align/lav_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align copying lib/bx/align/score.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align copying lib/bx/align/score_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align copying lib/bx/align/core.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align copying lib/bx/align/epo_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/cookbook copying lib/bx/cookbook/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/cookbook copying lib/bx/cookbook/doc_optparse.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/cookbook copying lib/bx/cookbook/attribute.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/cookbook creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/binary_file.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/seekbzip2.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/readlengths.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/cdb.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/cdb_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/filecache.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/seeklzop.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/seekbzip2_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/seeklzop_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/bgzf_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc copying lib/bx/misc/filecache_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/arrays copying lib/bx/arrays/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/arrays copying lib/bx/arrays/array_tree_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/arrays creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/phylo copying lib/bx/phylo/phast.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/phylo copying lib/bx/phylo/newick_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/phylo copying lib/bx/phylo/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/phylo copying lib/bx/phylo/phast_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/phylo copying lib/bx/phylo/newick.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/phylo creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm copying lib/bx/pwm/pwm_score_maf.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm copying lib/bx/pwm/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm copying lib/bx/pwm/position_weight_matrix.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm copying lib/bx/pwm/pwm_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm copying lib/bx/pwm/maf_select_motifs.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm copying lib/bx/pwm/pwm_score_positions.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/logo copying lib/bx/motif/logo/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/logo creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/io copying lib/bx/motif/io/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/io copying lib/bx/motif/io/transfac.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/io copying lib/bx/motif/io/transfac_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/io creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations copying lib/bx/intervals/operations/complement.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations copying lib/bx/intervals/operations/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations copying lib/bx/intervals/operations/quicksect.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations copying lib/bx/intervals/operations/intersect.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations copying lib/bx/intervals/operations/merge.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations copying lib/bx/intervals/operations/coverage.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations copying lib/bx/intervals/operations/join.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations copying lib/bx/intervals/operations/subtract.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations copying lib/bx/intervals/operations/base_coverage.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations copying lib/bx/intervals/operations/find_clusters.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations copying lib/bx/intervals/operations/concat.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask copying lib/bx/align/sitemask/quality.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask copying lib/bx/align/sitemask/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask copying lib/bx/align/sitemask/core.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask copying lib/bx/align/sitemask/cpg.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask creating build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/tools copying lib/bx/align/tools/chop.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/tools copying lib/bx/align/tools/__init__.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/tools copying lib/bx/align/tools/fuse.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/tools copying lib/bx/align/tools/tile.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/tools copying lib/bx/align/tools/thread.py -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/tools running egg_info writing lib/bx_python.egg-info/PKG-INFO writing dependency_links to lib/bx_python.egg-info/dependency_links.txt writing requirements to lib/bx_python.egg-info/requires.txt writing top-level names to lib/bx_python.egg-info/top_level.txt reading manifest file 'lib/bx_python.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'lib/bx_python.egg-info/SOURCES.txt' copying lib/bx/motif/logo/template.ps -> build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/logo running build_ext Compiling lib/bx/bitset.pyx because it changed. [1/1] Cythonizing lib/bx/bitset.pyx building 'bx.bitset' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311 creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/kent cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python3.11 -c lib/bx/bitset.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bitset.o cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python3.11 -c src/binBits.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/binBits.o cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python3.11 -c src/kent/bits.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/kent/bits.o cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python3.11 -c src/kent/common.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/kent/common.o cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bitset.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/binBits.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/kent/bits.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/kent/common.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bitset.cpython-311.so Compiling lib/bx/intervals/intersection.pyx because it changed. [1/1] Cythonizing lib/bx/intervals/intersection.pyx building 'bx.intervals.intersection' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/intervals cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c lib/bx/intervals/intersection.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/intervals/intersection.o lib/bx/intervals/intersection.c:3701:5: warning: code will never be executed [-Wunreachable-code] 3701 | PyErr_SetString(PyExc_ZeroDivisionError, "float division"); | ^~~~~~~~~~~~~~~ 1 warning generated. cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/intervals/intersection.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/intersection.cpython-311.so Compiling lib/bx/align/_core.pyx because it changed. [1/1] Cythonizing lib/bx/align/_core.pyx building 'bx.align._core' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/align cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c lib/bx/align/_core.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/align/_core.o cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/align/_core.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/_core.cpython-311.so Compiling lib/bx/seq/_nib.pyx because it changed. [1/1] Cythonizing lib/bx/seq/_nib.pyx building 'bx.seq._nib' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/seq cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c lib/bx/seq/_nib.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/seq/_nib.o cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/seq/_nib.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/_nib.cpython-311.so Compiling lib/bx/seq/_twobit.pyx because it changed. [1/1] Cythonizing lib/bx/seq/_twobit.pyx building 'bx.seq._twobit' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c lib/bx/seq/_twobit.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/seq/_twobit.o cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/seq/_twobit.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/_twobit.cpython-311.so Compiling lib/bx/_seqmapping.pyx because it changed. [1/1] Cythonizing lib/bx/_seqmapping.pyx building 'bx._seqmapping' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c lib/bx/_seqmapping.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/_seqmapping.o cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/_seqmapping.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/_seqmapping.cpython-311.so Compiling lib/bx/misc/bgzf.pyx because it changed. [1/1] Cythonizing lib/bx/misc/bgzf.pyx building 'bx.misc.bgzf' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/misc creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/samtools cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc/samtools -I/usr/local/include/python3.11 -c lib/bx/misc/bgzf.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/misc/bgzf.o cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc/samtools -I/usr/local/include/python3.11 -c src/samtools/bgzf.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/samtools/bgzf.o src/samtools/bgzf.c:247:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 139 to -117 [-Wconstant-conversion] 247 | buffer[1] = GZIP_ID2; | ~ ^~~~~~~~ src/samtools/bgzf.c:255:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 255 to -1 [-Wconstant-conversion] 255 | buffer[9] = OS_UNKNOWN; | ~ ^~~~~~~~~~ src/samtools/bgzf.c:422:40: warning: comparison of integers of different signs: 'khint_t' (aka 'unsigned int') and 'int' [-Wsign-compare] 422 | if ((kh_size(h) + 1) * MAX_BLOCK_SIZE > fp->cache_size) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~ src/samtools/bgzf.c:462:15: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] 462 | if (count != sizeof(header)) { | ~~~~~ ^ ~~~~~~~~~~~~~~ 4 warnings generated. cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/misc/bgzf.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/samtools/bgzf.o -L/usr/local/lib -lz -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/bgzf.cpython-311.so Compiling lib/bx/intervals/cluster.pyx because it changed. [1/1] Cythonizing lib/bx/intervals/cluster.pyx building 'bx.intervals.cluster' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.11 -c lib/bx/intervals/cluster.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/intervals/cluster.o cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.11 -c src/cluster.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/cluster.o cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/intervals/cluster.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/cluster.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/cluster.cpython-311.so Compiling lib/bx/pwm/_position_weight_matrix.pyx because it changed. [1/1] Cythonizing lib/bx/pwm/_position_weight_matrix.pyx building 'bx.pwm._position_weight_matrix' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/pwm cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.11 -c lib/bx/pwm/_position_weight_matrix.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/pwm/_position_weight_matrix.o cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.11 -c src/pwm_utils.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/pwm_utils.o src/pwm_utils.c:12:29: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] 12 | if (strlen(argv[2]) != string_size) { | ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~ 1 warning generated. cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/pwm/_position_weight_matrix.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/pwm_utils.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm/_position_weight_matrix.cpython-311.so Compiling lib/bx/motif/_pwm.pyx because it changed. [1/1] Cythonizing lib/bx/motif/_pwm.pyx building 'bx.motif._pwm' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/motif cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c lib/bx/motif/_pwm.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/motif/_pwm.o In file included from lib/bx/motif/_pwm.c:1138: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ 1 warning generated. cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/motif/_pwm.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/_pwm.cpython-311.so Compiling lib/bx/arrays/array_tree.pyx because it changed. [1/1] Cythonizing lib/bx/arrays/array_tree.pyx building 'bx.arrays.array_tree' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/arrays cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c lib/bx/arrays/array_tree.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/arrays/array_tree.o In file included from lib/bx/arrays/array_tree.c:1147: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ 1 warning generated. cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/arrays/array_tree.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/arrays/array_tree.cpython-311.so Compiling lib/bx/bbi/bpt_file.pyx because it changed. [1/1] Cythonizing lib/bx/bbi/bpt_file.pyx building 'bx.bbi.bpt_file' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bbi cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c lib/bx/bbi/bpt_file.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bbi/bpt_file.o cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bbi/bpt_file.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/bpt_file.cpython-311.so Compiling lib/bx/bbi/cirtree_file.pyx because it changed. [1/1] Cythonizing lib/bx/bbi/cirtree_file.pyx building 'bx.bbi.cirtree_file' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c lib/bx/bbi/cirtree_file.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bbi/cirtree_file.o cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bbi/cirtree_file.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/cirtree_file.cpython-311.so Compiling lib/bx/bbi/bbi_file.pyx because it changed. [1/1] Cythonizing lib/bx/bbi/bbi_file.pyx building 'bx.bbi.bbi_file' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c lib/bx/bbi/bbi_file.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bbi/bbi_file.o In file included from lib/bx/bbi/bbi_file.c:1147: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ 1 warning generated. cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bbi/bbi_file.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/bbi_file.cpython-311.so Compiling lib/bx/bbi/bigwig_file.pyx because it changed. [1/1] Cythonizing lib/bx/bbi/bigwig_file.pyx building 'bx.bbi.bigwig_file' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c lib/bx/bbi/bigwig_file.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bbi/bigwig_file.o In file included from lib/bx/bbi/bigwig_file.c:1147: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ lib/bx/bbi/bigwig_file.c:5809:29: warning: comparison of integers of different signs: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' (aka 'unsigned int') [-Wsign-compare] 5809 | __pyx_t_14 = (__pyx_v_s < __pyx_v_self->start); | ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~ lib/bx/bbi/bigwig_file.c:5838:29: warning: comparison of integers of different signs: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' (aka 'unsigned int') [-Wsign-compare] 5838 | __pyx_t_14 = (__pyx_v_e > __pyx_v_self->end); | ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~ lib/bx/bbi/bigwig_file.c:8025:76: warning: comparison of integers of different signs: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' (aka 'unsigned int') [-Wsign-compare] 8025 | for (__pyx_v_i = (__pyx_v_s - __pyx_v_self->__pyx_base.start); __pyx_v_i < __pyx_t_2; __pyx_v_i++) { | ~~~~~~~~~ ^ ~~~~~~~~~ 4 warnings generated. cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bbi/bigwig_file.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/bigwig_file.cpython-311.so Compiling lib/bx/bbi/bigbed_file.pyx because it changed. [1/1] Cythonizing lib/bx/bbi/bigbed_file.pyx building 'bx.bbi.bigbed_file' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c lib/bx/bbi/bigbed_file.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bbi/bigbed_file.o In file included from lib/bx/bbi/bigbed_file.c:1147: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ 1 warning generated. cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/bbi/bigbed_file.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/bigbed_file.cpython-311.so Compiling lib/bx/align/_epo.pyx because it changed. [1/1] Cythonizing lib/bx/align/_epo.pyx building 'bx.align._epo' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c lib/bx/align/_epo.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/align/_epo.o In file included from lib/bx/align/_epo.c:1147: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ lib/bx/align/_epo.c:8569:236: warning: comparison of integers of different signs: '__pyx_t_5numpy_uint64_t' (aka 'unsigned long') and 'Py_ssize_t' (aka 'long') [-Wsign-compare] 8569 | __pyx_t_6 = ((*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_uint64_t *, __pyx_pybuffernd_elements.rcbuffer->pybuffer.buf, __pyx_t_14, __pyx_pybuffernd_elements.diminfo[0].strides, __pyx_t_15, __pyx_pybuffernd_elements.diminfo[1].strides)) <= __pyx_v_cen); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~ 2 warnings generated. cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/align/_epo.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/_epo.cpython-311.so Compiling lib/bx/arrays/bed.pyx because it changed. [1/1] Cythonizing lib/bx/arrays/bed.pyx building 'bx.arrays.bed' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c lib/bx/arrays/bed.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/arrays/bed.o cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/arrays/bed.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/arrays/bed.cpython-311.so warning: lib/bx/arrays/wiggle.pyx:94:20: Unreachable code Compiling lib/bx/arrays/wiggle.pyx because it changed. [1/1] Cythonizing lib/bx/arrays/wiggle.pyx building 'bx.arrays.wiggle' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c lib/bx/arrays/wiggle.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/arrays/wiggle.o cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/arrays/wiggle.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/arrays/wiggle.cpython-311.so Compiling lib/bx/align/sitemask/_cpg.pyx because it changed. [1/1] Cythonizing lib/bx/align/sitemask/_cpg.pyx building 'bx.align.sitemask._cpg' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/align/sitemask cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c lib/bx/align/sitemask/_cpg.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/align/sitemask/_cpg.o cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.11 -c lib/bx/align/sitemask/find_cpg.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/align/sitemask/find_cpg.o cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/align/sitemask/_cpg.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/align/sitemask/find_cpg.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask/_cpg.cpython-311.so Compiling lib/bx/intseq/ngramcount.pyx because it changed. [1/1] Cythonizing lib/bx/intseq/ngramcount.pyx building 'bx.intseq.ngramcount' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/intseq cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.11 -c lib/bx/intseq/ngramcount.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/intseq/ngramcount.o lib/bx/intseq/ngramcount.c:2710:46: warning: comparison of integers of different signs: 'char' and 'Py_UCS4' (aka 'unsigned int') [-Wsign-compare] 2710 | __pyx_t_3 = (__pyx_v_ints_desc->typekind == __pyx_t_5); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ lib/bx/intseq/ngramcount.c:2973:46: warning: comparison of integers of different signs: 'char' and 'Py_UCS4' (aka 'unsigned int') [-Wsign-compare] 2973 | __pyx_t_3 = (__pyx_v_rval_desc->typekind == __pyx_t_5); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ 2 warnings generated. cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/intseq/ngramcount.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intseq/ngramcount.cpython-311.so Compiling lib/bx/misc/_seekbzip2.pyx because it changed. [1/1] Cythonizing lib/bx/misc/_seekbzip2.pyx building 'bx.misc._seekbzip2' extension creating build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/bunzip cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc/bunzip -I/usr/local/include/python3.11 -c lib/bx/misc/_seekbzip2.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/misc/_seekbzip2.o cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Isrc/bunzip -I/usr/local/include/python3.11 -c src/bunzip/micro-bunzip.c -o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/bunzip/micro-bunzip.o src/bunzip/micro-bunzip.c:99:26: warning: comparison of integers of different signs: 'unsigned int' and 'char' [-Wsign-compare] 99 | while (bd->inbufBitCount dbufSize) return RETVAL_DATA_ERROR; | ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~ src/bunzip/micro-bunzip.c:298:27: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 298 | while (bd->inbufBitCountmaxLen) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ src/bunzip/micro-bunzip.c:400:13: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 400 | if(origPtr>=dbufCount) return RETVAL_DATA_ERROR; | ~~~~~~~^ ~~~~~~~~~ src/bunzip/micro-bunzip.c:629:12: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign] 629 | bd->inbuf=inbuf; | ^~~~~~ 5 warnings generated. cc -shared -L/usr/local/lib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/lib/bx/misc/_seekbzip2.o build/temp.freebsd-13.5-RELEASE-p7-amd64-cpython-311/src/bunzip/micro-bunzip.o -L/usr/local/lib -o build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/_seekbzip2.cpython-311.so running build_scripts creating build/scripts-3.11 copying and adjusting scripts/wiggle_to_binned_array.py -> build/scripts-3.11 copying and adjusting scripts/maf_col_counts.py -> build/scripts-3.11 copying and adjusting scripts/table_add_column.py -> build/scripts-3.11 copying and adjusting scripts/bed_rand_intersect.py -> build/scripts-3.11 copying and adjusting scripts/nib_intervals_to_fasta.py -> build/scripts-3.11 copying and adjusting scripts/bnMapper.py -> build/scripts-3.11 copying and adjusting scripts/bed_merge_overlapping.py -> build/scripts-3.11 copying and adjusting scripts/wiggle_to_array_tree.py -> build/scripts-3.11 copying and adjusting scripts/bed_bigwig_profile.py -> build/scripts-3.11 copying and adjusting scripts/wiggle_to_simple.py -> build/scripts-3.11 copying and adjusting scripts/maf_chunk.py -> build/scripts-3.11 copying and adjusting scripts/maf_col_counts_all.py -> build/scripts-3.11 copying and adjusting scripts/aggregate_scores_in_intervals.py -> build/scripts-3.11 copying and adjusting scripts/wiggle_to_chr_binned_array.py -> build/scripts-3.11 copying and adjusting scripts/maf_truncate.py -> build/scripts-3.11 copying and adjusting scripts/axt_to_fasta.py -> build/scripts-3.11 copying and adjusting scripts/maf_extract_chrom_ranges.py -> build/scripts-3.11 copying and adjusting scripts/maf_count.py -> build/scripts-3.11 copying and adjusting scripts/maf_region_coverage_by_src.py -> build/scripts-3.11 copying and adjusting scripts/gene_fourfold_sites.py -> build/scripts-3.11 copying and adjusting scripts/interval_join.py -> build/scripts-3.11 copying and adjusting scripts/mask_quality.py -> build/scripts-3.11 copying and adjusting scripts/maf_select.py -> build/scripts-3.11 copying and adjusting scripts/nib_length.py -> build/scripts-3.11 copying and adjusting scripts/bed_count_by_interval.py -> build/scripts-3.11 copying and adjusting scripts/maf_gap_frequency.py -> build/scripts-3.11 copying and adjusting scripts/maf_tile_2bit.py -> build/scripts-3.11 copying and adjusting scripts/maf_tile_2.py -> build/scripts-3.11 copying and adjusting scripts/maf_mask_cpg.py -> build/scripts-3.11 copying and adjusting scripts/div_snp_table_chr.py -> build/scripts-3.11 copying and adjusting scripts/maf_chop.py -> build/scripts-3.11 copying and adjusting scripts/lav_to_maf.py -> build/scripts-3.11 copying and adjusting scripts/bed_coverage.py -> build/scripts-3.11 copying and adjusting scripts/bed_diff_basewise_summary.py -> build/scripts-3.11 copying and adjusting scripts/maf_mapping_word_frequency.py -> build/scripts-3.11 copying and adjusting scripts/maf_build_index.py -> build/scripts-3.11 copying and adjusting scripts/tfloc_summary.py -> build/scripts-3.11 copying and adjusting scripts/bed_intersect.py -> build/scripts-3.11 copying and adjusting scripts/get_scores_in_intervals.py -> build/scripts-3.11 copying and adjusting scripts/bed_build_windows.py -> build/scripts-3.11 copying and adjusting scripts/maf_print_chroms.py -> build/scripts-3.11 copying and adjusting scripts/maf_div_sites.py -> build/scripts-3.11 copying and adjusting scripts/lav_to_axt.py -> build/scripts-3.11 copying and adjusting scripts/maf_to_concat_fasta.py -> build/scripts-3.11 copying and adjusting scripts/prefix_lines.py -> build/scripts-3.11 copying and adjusting scripts/maf_mean_length_ungapped_piece.py -> build/scripts-3.11 copying and adjusting scripts/pretty_table.py -> build/scripts-3.11 copying and adjusting scripts/bed_extend_to.py -> build/scripts-3.11 copying and adjusting scripts/bed_subtract_basewise.py -> build/scripts-3.11 copying and adjusting scripts/maf_to_axt.py -> build/scripts-3.11 copying and adjusting scripts/maf_word_frequency.py -> build/scripts-3.11 copying and adjusting scripts/maf_covered_regions.py -> build/scripts-3.11 copying and adjusting scripts/line_select.py -> build/scripts-3.11 copying and adjusting scripts/maf_to_fasta.py -> build/scripts-3.11 copying and adjusting scripts/maf_species_in_all_files.py -> build/scripts-3.11 copying and adjusting scripts/maf_thread_for_species.py -> build/scripts-3.11 copying and adjusting scripts/table_filter.py -> build/scripts-3.11 copying and adjusting scripts/bed_count_overlapping.py -> build/scripts-3.11 copying and adjusting scripts/interval_count_intersections.py -> build/scripts-3.11 copying and adjusting scripts/maf_percent_identity.py -> build/scripts-3.11 copying and adjusting scripts/int_seqs_to_char_strings.py -> build/scripts-3.11 copying and adjusting scripts/bed_complement.py -> build/scripts-3.11 copying and adjusting scripts/maf_gc_content.py -> build/scripts-3.11 copying and adjusting scripts/maf_interval_alignibility.py -> build/scripts-3.11 copying and adjusting scripts/maf_print_scores.py -> build/scripts-3.11 copying and adjusting scripts/maf_to_int_seqs.py -> build/scripts-3.11 copying and adjusting scripts/nib_chrom_intervals_to_fasta.py -> build/scripts-3.11 copying and adjusting scripts/maf_split_by_src.py -> build/scripts-3.11 copying and adjusting scripts/align_print_template.py -> build/scripts-3.11 copying and adjusting scripts/maf_shuffle_columns.py -> build/scripts-3.11 copying and adjusting scripts/mMK_bitset.py -> build/scripts-3.11 copying and adjusting scripts/maf_translate_chars.py -> build/scripts-3.11 copying and adjusting scripts/maf_percent_columns_matching.py -> build/scripts-3.11 copying and adjusting scripts/maf_filter_max_wc.py -> build/scripts-3.11 copying and adjusting scripts/bed_coverage_by_interval.py -> build/scripts-3.11 copying and adjusting scripts/bed_intersect_basewise.py -> build/scripts-3.11 copying and adjusting scripts/one_field_per_line.py -> build/scripts-3.11 copying and adjusting scripts/maf_drop_overlapping.py -> build/scripts-3.11 copying and adjusting scripts/find_in_sorted_file.py -> build/scripts-3.11 copying and adjusting scripts/qv_to_bqv.py -> build/scripts-3.11 copying and adjusting scripts/axt_to_maf.py -> build/scripts-3.11 copying and adjusting scripts/axt_extract_ranges.py -> build/scripts-3.11 copying and adjusting scripts/maf_tile.py -> build/scripts-3.11 copying and adjusting scripts/maf_covered_ranges.py -> build/scripts-3.11 copying and adjusting scripts/maf_filter.py -> build/scripts-3.11 copying and adjusting scripts/axt_to_lav.py -> build/scripts-3.11 copying and adjusting scripts/maf_extract_ranges.py -> build/scripts-3.11 copying and adjusting scripts/maf_extract_ranges_indexed.py -> build/scripts-3.11 copying and adjusting scripts/maf_randomize.py -> build/scripts-3.11 copying and adjusting scripts/ucsc_gene_table_to_intervals.py -> build/scripts-3.11 copying and adjusting scripts/out_to_chain.py -> build/scripts-3.11 copying and adjusting scripts/random_lines.py -> build/scripts-3.11 copying and adjusting scripts/maf_limit_to_species.py -> build/scripts-3.11 copying and adjusting scripts/lzop_build_offset_table.py -> build/scripts-3.11 changing mode of build/scripts-3.11/wiggle_to_binned_array.py from 644 to 755 changing mode of build/scripts-3.11/maf_col_counts.py from 644 to 755 changing mode of build/scripts-3.11/table_add_column.py from 644 to 755 changing mode of build/scripts-3.11/bed_rand_intersect.py from 644 to 755 changing mode of build/scripts-3.11/nib_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.11/bnMapper.py from 644 to 755 changing mode of build/scripts-3.11/bed_merge_overlapping.py from 644 to 755 changing mode of build/scripts-3.11/wiggle_to_array_tree.py from 644 to 755 changing mode of build/scripts-3.11/bed_bigwig_profile.py from 644 to 755 changing mode of build/scripts-3.11/wiggle_to_simple.py from 644 to 755 changing mode of build/scripts-3.11/maf_chunk.py from 644 to 755 changing mode of build/scripts-3.11/maf_col_counts_all.py from 644 to 755 changing mode of build/scripts-3.11/aggregate_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.11/wiggle_to_chr_binned_array.py from 644 to 755 changing mode of build/scripts-3.11/maf_truncate.py from 644 to 755 changing mode of build/scripts-3.11/axt_to_fasta.py from 644 to 755 changing mode of build/scripts-3.11/maf_extract_chrom_ranges.py from 644 to 755 changing mode of build/scripts-3.11/maf_count.py from 644 to 755 changing mode of build/scripts-3.11/maf_region_coverage_by_src.py from 644 to 755 changing mode of build/scripts-3.11/gene_fourfold_sites.py from 644 to 755 changing mode of build/scripts-3.11/interval_join.py from 644 to 755 changing mode of build/scripts-3.11/mask_quality.py from 644 to 755 changing mode of build/scripts-3.11/maf_select.py from 644 to 755 changing mode of build/scripts-3.11/nib_length.py from 644 to 755 changing mode of build/scripts-3.11/bed_count_by_interval.py from 644 to 755 changing mode of build/scripts-3.11/maf_gap_frequency.py from 644 to 755 changing mode of build/scripts-3.11/maf_tile_2bit.py from 644 to 755 changing mode of build/scripts-3.11/maf_tile_2.py from 644 to 755 changing mode of build/scripts-3.11/maf_mask_cpg.py from 644 to 755 changing mode of build/scripts-3.11/div_snp_table_chr.py from 644 to 755 changing mode of build/scripts-3.11/maf_chop.py from 644 to 755 changing mode of build/scripts-3.11/lav_to_maf.py from 644 to 755 changing mode of build/scripts-3.11/bed_coverage.py from 644 to 755 changing mode of build/scripts-3.11/bed_diff_basewise_summary.py from 644 to 755 changing mode of build/scripts-3.11/maf_mapping_word_frequency.py from 644 to 755 changing mode of build/scripts-3.11/maf_build_index.py from 644 to 755 changing mode of build/scripts-3.11/tfloc_summary.py from 644 to 755 changing mode of build/scripts-3.11/bed_intersect.py from 644 to 755 changing mode of build/scripts-3.11/get_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.11/bed_build_windows.py from 644 to 755 changing mode of build/scripts-3.11/maf_print_chroms.py from 644 to 755 changing mode of build/scripts-3.11/maf_div_sites.py from 644 to 755 changing mode of build/scripts-3.11/lav_to_axt.py from 644 to 755 changing mode of build/scripts-3.11/maf_to_concat_fasta.py from 644 to 755 changing mode of build/scripts-3.11/prefix_lines.py from 644 to 755 changing mode of build/scripts-3.11/maf_mean_length_ungapped_piece.py from 644 to 755 changing mode of build/scripts-3.11/pretty_table.py from 644 to 755 changing mode of build/scripts-3.11/bed_extend_to.py from 644 to 755 changing mode of build/scripts-3.11/bed_subtract_basewise.py from 644 to 755 changing mode of build/scripts-3.11/maf_to_axt.py from 644 to 755 changing mode of build/scripts-3.11/maf_word_frequency.py from 644 to 755 changing mode of build/scripts-3.11/maf_covered_regions.py from 644 to 755 changing mode of build/scripts-3.11/line_select.py from 644 to 755 changing mode of build/scripts-3.11/maf_to_fasta.py from 644 to 755 changing mode of build/scripts-3.11/maf_species_in_all_files.py from 644 to 755 changing mode of build/scripts-3.11/maf_thread_for_species.py from 644 to 755 changing mode of build/scripts-3.11/table_filter.py from 644 to 755 changing mode of build/scripts-3.11/bed_count_overlapping.py from 644 to 755 changing mode of build/scripts-3.11/interval_count_intersections.py from 644 to 755 changing mode of build/scripts-3.11/maf_percent_identity.py from 644 to 755 changing mode of build/scripts-3.11/int_seqs_to_char_strings.py from 644 to 755 changing mode of build/scripts-3.11/bed_complement.py from 644 to 755 changing mode of build/scripts-3.11/maf_gc_content.py from 644 to 755 changing mode of build/scripts-3.11/maf_interval_alignibility.py from 644 to 755 changing mode of build/scripts-3.11/maf_print_scores.py from 644 to 755 changing mode of build/scripts-3.11/maf_to_int_seqs.py from 644 to 755 changing mode of build/scripts-3.11/nib_chrom_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.11/maf_split_by_src.py from 644 to 755 changing mode of build/scripts-3.11/align_print_template.py from 644 to 755 changing mode of build/scripts-3.11/maf_shuffle_columns.py from 644 to 755 changing mode of build/scripts-3.11/mMK_bitset.py from 644 to 755 changing mode of build/scripts-3.11/maf_translate_chars.py from 644 to 755 changing mode of build/scripts-3.11/maf_percent_columns_matching.py from 644 to 755 changing mode of build/scripts-3.11/maf_filter_max_wc.py from 644 to 755 changing mode of build/scripts-3.11/bed_coverage_by_interval.py from 644 to 755 changing mode of build/scripts-3.11/bed_intersect_basewise.py from 644 to 755 changing mode of build/scripts-3.11/one_field_per_line.py from 644 to 755 changing mode of build/scripts-3.11/maf_drop_overlapping.py from 644 to 755 changing mode of build/scripts-3.11/find_in_sorted_file.py from 644 to 755 changing mode of build/scripts-3.11/qv_to_bqv.py from 644 to 755 changing mode of build/scripts-3.11/axt_to_maf.py from 644 to 755 changing mode of build/scripts-3.11/axt_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.11/maf_tile.py from 644 to 755 changing mode of build/scripts-3.11/maf_covered_ranges.py from 644 to 755 changing mode of build/scripts-3.11/maf_filter.py from 644 to 755 changing mode of build/scripts-3.11/axt_to_lav.py from 644 to 755 changing mode of build/scripts-3.11/maf_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.11/maf_extract_ranges_indexed.py from 644 to 755 changing mode of build/scripts-3.11/maf_randomize.py from 644 to 755 changing mode of build/scripts-3.11/ucsc_gene_table_to_intervals.py from 644 to 755 changing mode of build/scripts-3.11/out_to_chain.py from 644 to 755 changing mode of build/scripts-3.11/random_lines.py from 644 to 755 changing mode of build/scripts-3.11/maf_limit_to_species.py from 644 to 755 changing mode of build/scripts-3.11/lzop_build_offset_table.py from 644 to 755 installing to build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel running install running install_lib creating build/bdist.freebsd-13.5-RELEASE-p7-amd64 creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_extras copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras/fpconst.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_extras copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_extras copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras/stats.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_extras copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras/lrucache.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_extras copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras/pstat.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_extras copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx_extras/fpconst_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_extras creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/bbi copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/bpt_file.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/bbi copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/bbi copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/bigwig_file.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/bbi copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/bigbed_file.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/bbi copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/bbi_file.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/bbi copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/bigwig_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/bbi copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bbi/cirtree_file.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/bbi copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/binned_array.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bitset_utils.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif/logo copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/logo/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif/logo copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/logo/template.ps -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif/logo copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/pwm_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/_pwm.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif/io copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/io/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif/io copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/io/transfac.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif/io copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/io/transfac_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif/io copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/motif/pwm.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/motif creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/seq_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/fasta_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/qdna_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/_twobit.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/twobit_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/nib_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/twobit.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/_nib.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/fasta.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/core.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/nib.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/qdna.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seq/seq.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/seq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/binned_array_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/tabular copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/tabular/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/tabular copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/tabular/io.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/tabular copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/gene_reader.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bitset_builders.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/filter.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/interval_index_file.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations/complement.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations/quicksect.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations/intersect.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations/merge.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations/coverage.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations/join.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations/subtract.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations/base_coverage.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations/find_clusters.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/operations/concat.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals/operations copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/cluster_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/io.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/intersection.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/intersection_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/random_intervals.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intervals/cluster.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intervals copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/_seqmapping.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/interval_index_file_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intseq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intseq/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intseq copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/intseq/ngramcount.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/intseq creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/axt.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/sitemask copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask/quality.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/sitemask copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask/sitemask_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/sitemask copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/sitemask copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask/_cpg.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/sitemask copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask/core.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/sitemask copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/sitemask/cpg.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/sitemask copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/epo.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/_core.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/lav.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/maf.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/maf_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/lav_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/tools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/tools/chop.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/tools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/tools/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/tools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/tools/fuse.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/tools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/tools/tile.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/tools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/tools/thread.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align/tools copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/score.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/score_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/_epo.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/core.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/align/epo_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/align creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/cookbook copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/cookbook/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/cookbook copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/cookbook/doc_optparse.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/cookbook copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/cookbook/attribute.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/cookbook creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/binary_file.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/seekbzip2.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/readlengths.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/cdb.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/bgzf.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/cdb_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/_seekbzip2.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/filecache.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/seeklzop.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/seekbzip2_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/seeklzop_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/bgzf_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/misc/filecache_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/misc creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/arrays copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/arrays/array_tree.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/arrays copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/arrays/bed.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/arrays copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/arrays/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/arrays copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/arrays/array_tree_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/arrays copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/arrays/wiggle.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/arrays copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seqmapping.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/phylo copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/phylo/phast.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/phylo copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/phylo/newick_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/phylo copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/phylo/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/phylo copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/phylo/phast_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/phylo copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/phylo/newick.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/phylo copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/seqmapping_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/wiggle.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/pwm copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm/bed_score_aligned_string.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/pwm copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm/_position_weight_matrix.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/pwm copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm/pwm_score_maf.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/pwm copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm/__init__.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/pwm copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm/position_weight_matrix.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/pwm copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm/pwm_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/pwm copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm/maf_select_motifs.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/pwm copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm/bed_score_aligned_pwm.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/pwm copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm/pwm_score_motifs.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/pwm copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/pwm/pwm_score_positions.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx/pwm copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bitset.cpython-311.so -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/wiggle_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx copying build/lib.freebsd-13.5-RELEASE-p7-amd64-cpython-311/bx/bitset_tests.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx running install_egg_info Copying lib/bx_python.egg-info to build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0-py3.11.egg-info running install_scripts creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/wiggle_to_binned_array.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_col_counts.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/table_add_column.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_rand_intersect.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/nib_intervals_to_fasta.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bnMapper.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_merge_overlapping.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/wiggle_to_array_tree.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_bigwig_profile.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/wiggle_to_simple.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_chunk.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_col_counts_all.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/aggregate_scores_in_intervals.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/wiggle_to_chr_binned_array.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_truncate.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/axt_to_fasta.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_extract_chrom_ranges.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_count.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_region_coverage_by_src.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/gene_fourfold_sites.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/interval_join.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/mask_quality.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_select.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/nib_length.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_count_by_interval.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_gap_frequency.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_tile_2bit.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_tile_2.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_mask_cpg.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/div_snp_table_chr.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_chop.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/lav_to_maf.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_coverage.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_diff_basewise_summary.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_mapping_word_frequency.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_build_index.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/tfloc_summary.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_intersect.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/get_scores_in_intervals.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_build_windows.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_print_chroms.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_div_sites.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/lav_to_axt.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_to_concat_fasta.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/prefix_lines.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_mean_length_ungapped_piece.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/pretty_table.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_extend_to.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_subtract_basewise.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_to_axt.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_word_frequency.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_covered_regions.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/line_select.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_to_fasta.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_species_in_all_files.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_thread_for_species.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/table_filter.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_count_overlapping.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/interval_count_intersections.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_percent_identity.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/int_seqs_to_char_strings.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_complement.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_gc_content.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_interval_alignibility.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_print_scores.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_to_int_seqs.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/nib_chrom_intervals_to_fasta.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_split_by_src.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/align_print_template.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_shuffle_columns.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/mMK_bitset.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_translate_chars.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_percent_columns_matching.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_filter_max_wc.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_coverage_by_interval.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/bed_intersect_basewise.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/one_field_per_line.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_drop_overlapping.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/find_in_sorted_file.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/qv_to_bqv.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/axt_to_maf.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/axt_extract_ranges.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_tile.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_covered_ranges.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_filter.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/axt_to_lav.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_extract_ranges.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_extract_ranges_indexed.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_randomize.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/ucsc_gene_table_to_intervals.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/out_to_chain.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/random_lines.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/maf_limit_to_species.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts copying build/scripts-3.11/lzop_build_offset_table.py -> build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/wiggle_to_binned_array.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_col_counts.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/table_add_column.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_rand_intersect.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/nib_intervals_to_fasta.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bnMapper.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_merge_overlapping.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/wiggle_to_array_tree.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_bigwig_profile.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/wiggle_to_simple.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_chunk.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_col_counts_all.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/aggregate_scores_in_intervals.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/wiggle_to_chr_binned_array.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_truncate.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/axt_to_fasta.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_extract_chrom_ranges.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_count.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_region_coverage_by_src.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/gene_fourfold_sites.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/interval_join.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/mask_quality.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_select.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/nib_length.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_count_by_interval.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_gap_frequency.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_tile_2bit.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_tile_2.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_mask_cpg.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/div_snp_table_chr.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_chop.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/lav_to_maf.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_coverage.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_diff_basewise_summary.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_mapping_word_frequency.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_build_index.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/tfloc_summary.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_intersect.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/get_scores_in_intervals.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_build_windows.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_print_chroms.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_div_sites.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/lav_to_axt.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_to_concat_fasta.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/prefix_lines.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_mean_length_ungapped_piece.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/pretty_table.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_extend_to.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_subtract_basewise.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_to_axt.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_word_frequency.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_covered_regions.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/line_select.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_to_fasta.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_species_in_all_files.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_thread_for_species.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/table_filter.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_count_overlapping.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/interval_count_intersections.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_percent_identity.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/int_seqs_to_char_strings.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_complement.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_gc_content.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_interval_alignibility.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_print_scores.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_to_int_seqs.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/nib_chrom_intervals_to_fasta.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_split_by_src.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/align_print_template.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_shuffle_columns.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/mMK_bitset.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_translate_chars.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_percent_columns_matching.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_filter_max_wc.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_coverage_by_interval.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/bed_intersect_basewise.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/one_field_per_line.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_drop_overlapping.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/find_in_sorted_file.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/qv_to_bqv.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/axt_to_maf.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/axt_extract_ranges.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_tile.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_covered_ranges.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_filter.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/axt_to_lav.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_extract_ranges.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_extract_ranges_indexed.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_randomize.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/ucsc_gene_table_to_intervals.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/out_to_chain.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/random_lines.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/maf_limit_to_species.py to 755 changing mode of build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.data/scripts/lzop_build_offset_table.py to 755 creating build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel/bx_python-0.14.0.dist-info/WHEEL creating '/wrkdirs/usr/ports/biology/py-bx-python/work-py311/bx_python-0.14.0/dist/tmprqr2d1x3/bx_python-0.14.0-cp311-cp311-freebsd_13_5_release_p7_amd64.whl' and adding 'build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel' to it adding 'bx/__init__.py' adding 'bx/_seqmapping.cpython-311.so' adding 'bx/binned_array.py' adding 'bx/binned_array_tests.py' adding 'bx/bitset.cpython-311.so' adding 'bx/bitset_builders.py' adding 'bx/bitset_tests.py' adding 'bx/bitset_utils.py' adding 'bx/filter.py' adding 'bx/gene_reader.py' adding 'bx/interval_index_file.py' adding 'bx/interval_index_file_tests.py' adding 'bx/seqmapping.py' adding 'bx/seqmapping_tests.py' adding 'bx/wiggle.py' adding 'bx/wiggle_tests.py' adding 'bx/align/__init__.py' adding 'bx/align/_core.cpython-311.so' adding 'bx/align/_epo.cpython-311.so' adding 'bx/align/axt.py' adding 'bx/align/core.py' adding 'bx/align/epo.py' adding 'bx/align/epo_tests.py' adding 'bx/align/lav.py' adding 'bx/align/lav_tests.py' adding 'bx/align/maf.py' adding 'bx/align/maf_tests.py' adding 'bx/align/score.py' adding 'bx/align/score_tests.py' adding 'bx/align/sitemask/__init__.py' adding 'bx/align/sitemask/_cpg.cpython-311.so' adding 'bx/align/sitemask/core.py' adding 'bx/align/sitemask/cpg.py' adding 'bx/align/sitemask/quality.py' adding 'bx/align/sitemask/sitemask_tests.py' adding 'bx/align/tools/__init__.py' adding 'bx/align/tools/chop.py' adding 'bx/align/tools/fuse.py' adding 'bx/align/tools/thread.py' adding 'bx/align/tools/tile.py' adding 'bx/arrays/__init__.py' adding 'bx/arrays/array_tree.cpython-311.so' adding 'bx/arrays/array_tree_tests.py' adding 'bx/arrays/bed.cpython-311.so' adding 'bx/arrays/wiggle.cpython-311.so' adding 'bx/bbi/__init__.py' adding 'bx/bbi/bbi_file.cpython-311.so' adding 'bx/bbi/bigbed_file.cpython-311.so' adding 'bx/bbi/bigwig_file.cpython-311.so' adding 'bx/bbi/bigwig_tests.py' adding 'bx/bbi/bpt_file.cpython-311.so' adding 'bx/bbi/cirtree_file.cpython-311.so' adding 'bx/cookbook/__init__.py' adding 'bx/cookbook/attribute.py' adding 'bx/cookbook/doc_optparse.py' adding 'bx/intervals/__init__.py' adding 'bx/intervals/cluster.cpython-311.so' adding 'bx/intervals/cluster_tests.py' adding 'bx/intervals/intersection.cpython-311.so' adding 'bx/intervals/intersection_tests.py' adding 'bx/intervals/io.py' adding 'bx/intervals/random_intervals.py' adding 'bx/intervals/operations/__init__.py' adding 'bx/intervals/operations/base_coverage.py' adding 'bx/intervals/operations/complement.py' adding 'bx/intervals/operations/concat.py' adding 'bx/intervals/operations/coverage.py' adding 'bx/intervals/operations/find_clusters.py' adding 'bx/intervals/operations/intersect.py' adding 'bx/intervals/operations/join.py' adding 'bx/intervals/operations/merge.py' adding 'bx/intervals/operations/quicksect.py' adding 'bx/intervals/operations/subtract.py' adding 'bx/intseq/__init__.py' adding 'bx/intseq/ngramcount.cpython-311.so' adding 'bx/misc/__init__.py' adding 'bx/misc/_seekbzip2.cpython-311.so' adding 'bx/misc/bgzf.cpython-311.so' adding 'bx/misc/bgzf_tests.py' adding 'bx/misc/binary_file.py' adding 'bx/misc/cdb.py' adding 'bx/misc/cdb_tests.py' adding 'bx/misc/filecache.py' adding 'bx/misc/filecache_tests.py' adding 'bx/misc/readlengths.py' adding 'bx/misc/seekbzip2.py' adding 'bx/misc/seekbzip2_tests.py' adding 'bx/misc/seeklzop.py' adding 'bx/misc/seeklzop_tests.py' adding 'bx/motif/__init__.py' adding 'bx/motif/_pwm.cpython-311.so' adding 'bx/motif/pwm.py' adding 'bx/motif/pwm_tests.py' adding 'bx/motif/io/__init__.py' adding 'bx/motif/io/transfac.py' adding 'bx/motif/io/transfac_tests.py' adding 'bx/motif/logo/__init__.py' adding 'bx/motif/logo/template.ps' adding 'bx/phylo/__init__.py' adding 'bx/phylo/newick.py' adding 'bx/phylo/newick_tests.py' adding 'bx/phylo/phast.py' adding 'bx/phylo/phast_tests.py' adding 'bx/pwm/__init__.py' adding 'bx/pwm/_position_weight_matrix.cpython-311.so' adding 'bx/pwm/bed_score_aligned_pwm.py' adding 'bx/pwm/bed_score_aligned_string.py' adding 'bx/pwm/maf_select_motifs.py' adding 'bx/pwm/position_weight_matrix.py' adding 'bx/pwm/pwm_score_maf.py' adding 'bx/pwm/pwm_score_motifs.py' adding 'bx/pwm/pwm_score_positions.py' adding 'bx/pwm/pwm_tests.py' adding 'bx/seq/__init__.py' adding 'bx/seq/_nib.cpython-311.so' adding 'bx/seq/_twobit.cpython-311.so' adding 'bx/seq/core.py' adding 'bx/seq/fasta.py' adding 'bx/seq/fasta_tests.py' adding 'bx/seq/nib.py' adding 'bx/seq/nib_tests.py' adding 'bx/seq/qdna.py' adding 'bx/seq/qdna_tests.py' adding 'bx/seq/seq.py' adding 'bx/seq/seq_tests.py' adding 'bx/seq/twobit.py' adding 'bx/seq/twobit_tests.py' adding 'bx/tabular/__init__.py' adding 'bx/tabular/io.py' adding 'bx_extras/__init__.py' adding 'bx_extras/fpconst.py' adding 'bx_extras/fpconst_tests.py' adding 'bx_extras/lrucache.py' adding 'bx_extras/pstat.py' adding 'bx_extras/stats.py' adding 'bx_python-0.14.0.data/scripts/aggregate_scores_in_intervals.py' adding 'bx_python-0.14.0.data/scripts/align_print_template.py' adding 'bx_python-0.14.0.data/scripts/axt_extract_ranges.py' adding 'bx_python-0.14.0.data/scripts/axt_to_fasta.py' adding 'bx_python-0.14.0.data/scripts/axt_to_lav.py' adding 'bx_python-0.14.0.data/scripts/axt_to_maf.py' adding 'bx_python-0.14.0.data/scripts/bed_bigwig_profile.py' adding 'bx_python-0.14.0.data/scripts/bed_build_windows.py' adding 'bx_python-0.14.0.data/scripts/bed_complement.py' adding 'bx_python-0.14.0.data/scripts/bed_count_by_interval.py' adding 'bx_python-0.14.0.data/scripts/bed_count_overlapping.py' adding 'bx_python-0.14.0.data/scripts/bed_coverage.py' adding 'bx_python-0.14.0.data/scripts/bed_coverage_by_interval.py' adding 'bx_python-0.14.0.data/scripts/bed_diff_basewise_summary.py' adding 'bx_python-0.14.0.data/scripts/bed_extend_to.py' adding 'bx_python-0.14.0.data/scripts/bed_intersect.py' adding 'bx_python-0.14.0.data/scripts/bed_intersect_basewise.py' adding 'bx_python-0.14.0.data/scripts/bed_merge_overlapping.py' adding 'bx_python-0.14.0.data/scripts/bed_rand_intersect.py' adding 'bx_python-0.14.0.data/scripts/bed_subtract_basewise.py' adding 'bx_python-0.14.0.data/scripts/bnMapper.py' adding 'bx_python-0.14.0.data/scripts/div_snp_table_chr.py' adding 'bx_python-0.14.0.data/scripts/find_in_sorted_file.py' adding 'bx_python-0.14.0.data/scripts/gene_fourfold_sites.py' adding 'bx_python-0.14.0.data/scripts/get_scores_in_intervals.py' adding 'bx_python-0.14.0.data/scripts/int_seqs_to_char_strings.py' adding 'bx_python-0.14.0.data/scripts/interval_count_intersections.py' adding 'bx_python-0.14.0.data/scripts/interval_join.py' adding 'bx_python-0.14.0.data/scripts/lav_to_axt.py' adding 'bx_python-0.14.0.data/scripts/lav_to_maf.py' adding 'bx_python-0.14.0.data/scripts/line_select.py' adding 'bx_python-0.14.0.data/scripts/lzop_build_offset_table.py' adding 'bx_python-0.14.0.data/scripts/mMK_bitset.py' adding 'bx_python-0.14.0.data/scripts/maf_build_index.py' adding 'bx_python-0.14.0.data/scripts/maf_chop.py' adding 'bx_python-0.14.0.data/scripts/maf_chunk.py' adding 'bx_python-0.14.0.data/scripts/maf_col_counts.py' adding 'bx_python-0.14.0.data/scripts/maf_col_counts_all.py' adding 'bx_python-0.14.0.data/scripts/maf_count.py' adding 'bx_python-0.14.0.data/scripts/maf_covered_ranges.py' adding 'bx_python-0.14.0.data/scripts/maf_covered_regions.py' adding 'bx_python-0.14.0.data/scripts/maf_div_sites.py' adding 'bx_python-0.14.0.data/scripts/maf_drop_overlapping.py' adding 'bx_python-0.14.0.data/scripts/maf_extract_chrom_ranges.py' adding 'bx_python-0.14.0.data/scripts/maf_extract_ranges.py' adding 'bx_python-0.14.0.data/scripts/maf_extract_ranges_indexed.py' adding 'bx_python-0.14.0.data/scripts/maf_filter.py' adding 'bx_python-0.14.0.data/scripts/maf_filter_max_wc.py' adding 'bx_python-0.14.0.data/scripts/maf_gap_frequency.py' adding 'bx_python-0.14.0.data/scripts/maf_gc_content.py' adding 'bx_python-0.14.0.data/scripts/maf_interval_alignibility.py' adding 'bx_python-0.14.0.data/scripts/maf_limit_to_species.py' adding 'bx_python-0.14.0.data/scripts/maf_mapping_word_frequency.py' adding 'bx_python-0.14.0.data/scripts/maf_mask_cpg.py' adding 'bx_python-0.14.0.data/scripts/maf_mean_length_ungapped_piece.py' adding 'bx_python-0.14.0.data/scripts/maf_percent_columns_matching.py' adding 'bx_python-0.14.0.data/scripts/maf_percent_identity.py' adding 'bx_python-0.14.0.data/scripts/maf_print_chroms.py' adding 'bx_python-0.14.0.data/scripts/maf_print_scores.py' adding 'bx_python-0.14.0.data/scripts/maf_randomize.py' adding 'bx_python-0.14.0.data/scripts/maf_region_coverage_by_src.py' adding 'bx_python-0.14.0.data/scripts/maf_select.py' adding 'bx_python-0.14.0.data/scripts/maf_shuffle_columns.py' adding 'bx_python-0.14.0.data/scripts/maf_species_in_all_files.py' adding 'bx_python-0.14.0.data/scripts/maf_split_by_src.py' adding 'bx_python-0.14.0.data/scripts/maf_thread_for_species.py' adding 'bx_python-0.14.0.data/scripts/maf_tile.py' adding 'bx_python-0.14.0.data/scripts/maf_tile_2.py' adding 'bx_python-0.14.0.data/scripts/maf_tile_2bit.py' adding 'bx_python-0.14.0.data/scripts/maf_to_axt.py' adding 'bx_python-0.14.0.data/scripts/maf_to_concat_fasta.py' adding 'bx_python-0.14.0.data/scripts/maf_to_fasta.py' adding 'bx_python-0.14.0.data/scripts/maf_to_int_seqs.py' adding 'bx_python-0.14.0.data/scripts/maf_translate_chars.py' adding 'bx_python-0.14.0.data/scripts/maf_truncate.py' adding 'bx_python-0.14.0.data/scripts/maf_word_frequency.py' adding 'bx_python-0.14.0.data/scripts/mask_quality.py' adding 'bx_python-0.14.0.data/scripts/nib_chrom_intervals_to_fasta.py' adding 'bx_python-0.14.0.data/scripts/nib_intervals_to_fasta.py' adding 'bx_python-0.14.0.data/scripts/nib_length.py' adding 'bx_python-0.14.0.data/scripts/one_field_per_line.py' adding 'bx_python-0.14.0.data/scripts/out_to_chain.py' adding 'bx_python-0.14.0.data/scripts/prefix_lines.py' adding 'bx_python-0.14.0.data/scripts/pretty_table.py' adding 'bx_python-0.14.0.data/scripts/qv_to_bqv.py' adding 'bx_python-0.14.0.data/scripts/random_lines.py' adding 'bx_python-0.14.0.data/scripts/table_add_column.py' adding 'bx_python-0.14.0.data/scripts/table_filter.py' adding 'bx_python-0.14.0.data/scripts/tfloc_summary.py' adding 'bx_python-0.14.0.data/scripts/ucsc_gene_table_to_intervals.py' adding 'bx_python-0.14.0.data/scripts/wiggle_to_array_tree.py' adding 'bx_python-0.14.0.data/scripts/wiggle_to_binned_array.py' adding 'bx_python-0.14.0.data/scripts/wiggle_to_chr_binned_array.py' adding 'bx_python-0.14.0.data/scripts/wiggle_to_simple.py' adding 'bx_python-0.14.0.dist-info/LICENSE' adding 'bx_python-0.14.0.dist-info/METADATA' adding 'bx_python-0.14.0.dist-info/WHEEL' adding 'bx_python-0.14.0.dist-info/top_level.txt' adding 'bx_python-0.14.0.dist-info/RECORD' removing build/bdist.freebsd-13.5-RELEASE-p7-amd64/wheel Successfully built bx_python-0.14.0-cp311-cp311-freebsd_13_5_release_p7_amd64.whl =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-bx-python-0.14.0 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> py311-bx-python-0.14.0 depends on package: py311-pyparsing>0 - not found ===> Installing existing package /packages/All/py311-pyparsing-3.3.1.pkg [pkg.DaveG.ca] Installing py311-pyparsing-3.3.1... [pkg.DaveG.ca] Extracting py311-pyparsing-3.3.1: .......... done ===> py311-bx-python-0.14.0 depends on package: py311-pyparsing>0 - found ===> Returning to build of py311-bx-python-0.14.0 ===> py311-bx-python-0.14.0 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py311-bx-python-0.14.0 ===> Generating temporary packing list ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-01-23T15:37:00+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=6d475ab2dcd0' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for py311-bx-python-0.14.0 ===> Building py311-bx-python-0.14.0 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-bx-python-0.14.0 build of biology/py-bx-python@py311 | py311-bx-python-0.14.0 ended at Fri Jan 23 10:38:18 EST 2026 build time: 00:01:19