=>> Building biology/py-bx-python build started at Thu Mar 28 08:09:56 GMT 2024 port directory: /usr/ports/biology/py-bx-python package name: py39-bx-python-0.11.0 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 591 Feb 14 06:15 /usr/ports/biology/py-bx-python/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 3fad843b18 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 06 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/06/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py39 MAKE_ARGS= FLAVOR=py39 ---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/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py39 TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/py-bx-python/work-py39/.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-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py39 TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/py-bx-python/work-py39/.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-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=13.2 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/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 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--- 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 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 ===> py39-bx-python-0.11.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> py39-bx-python-0.11.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-bx-python-0.11.0 =========================================================================== =================================================== ===== 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 py39-bx-python-0.11.0 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py39-bx-python-0.11.0 for building => SHA256 Checksum OK for bx-python-0.11.0.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 py39-bx-python-0.11.0 for building ===> Extracting for py39-bx-python-0.11.0 => SHA256 Checksum OK for bx-python-0.11.0.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 py39-bx-python-0.11.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-bx-python-0.11.0 depends on package: py39-numpy>=1.16,1<1.26,1 - not found ===> Installing existing package /packages/All/py39-numpy-1.25.0_6,1.pkg [pkg-builder.dan.net.uk] Installing py39-numpy-1.25.0_6,1... [pkg-builder.dan.net.uk] `-- Installing gcc13-13.2.0_4... [pkg-builder.dan.net.uk] | `-- Installing binutils-2.40_5,1... [pkg-builder.dan.net.uk] | | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting binutils-2.40_5,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | | `-- Installing mpfr-4.2.1,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] `-- Extracting gcc13-13.2.0_4: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) [pkg-builder.dan.net.uk] `-- Installing openblas-0.3.25,2... [pkg-builder.dan.net.uk] `-- Extracting openblas-0.3.25,2: .......... done [pkg-builder.dan.net.uk] `-- Installing py39-setuptools-63.1.0_1... [pkg-builder.dan.net.uk] | `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] | `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting py39-setuptools-63.1.0_1: .......... done [pkg-builder.dan.net.uk] `-- Installing suitesparse-umfpack-6.3.2... [pkg-builder.dan.net.uk] | `-- Installing suitesparse-amd-3.3.1... [pkg-builder.dan.net.uk] | | `-- Installing suitesparse-config-7.6.1... [pkg-builder.dan.net.uk] | | `-- Extracting suitesparse-config-7.6.1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-amd-3.3.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing suitesparse-camd-3.3.1... [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-camd-3.3.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing suitesparse-ccolamd-3.3.2... [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-ccolamd-3.3.2: .......... done [pkg-builder.dan.net.uk] | `-- Installing suitesparse-cholmod-5.2.0... [pkg-builder.dan.net.uk] | | `-- Installing suitesparse-colamd-3.3.2... [pkg-builder.dan.net.uk] | | `-- Extracting suitesparse-colamd-3.3.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-cholmod-5.2.0: .......... done [pkg-builder.dan.net.uk] `-- Extracting suitesparse-umfpack-6.3.2: .......... done [pkg-builder.dan.net.uk] Extracting py39-numpy-1.25.0_6,1: .......... done ===== Message from gcc13-13.2.0_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/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> py39-bx-python-0.11.0 depends on package: py39-numpy>=1.16,1<1.26,1 - found ===> Returning to build of py39-bx-python-0.11.0 ===> py39-bx-python-0.11.0 depends on executable: cython-3.9 - not found ===> Installing existing package /packages/All/py39-cython-0.29.37.pkg [pkg-builder.dan.net.uk] Installing py39-cython-0.29.37... [pkg-builder.dan.net.uk] Extracting py39-cython-0.29.37: .......... done ===> py39-bx-python-0.11.0 depends on executable: cython-3.9 - found ===> Returning to build of py39-bx-python-0.11.0 ===> py39-bx-python-0.11.0 depends on package: py39-setuptools>=63.1.0 - found ===> py39-bx-python-0.11.0 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py39-bx-python-0.11.0 running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py39-bx-python-0.11.0 running build running build_py creating build creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39 copying lib/psyco_full.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39 creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras copying lib/bx_extras/fpconst.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras copying lib/bx_extras/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras copying lib/bx_extras/stats.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras copying lib/bx_extras/lrucache.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras copying lib/bx_extras/pyparsing.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras copying lib/bx_extras/pstat.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras copying lib/bx_extras/fpconst_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/binned_array.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/bitset_utils.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/binned_array_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/gene_reader.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/bitset_builders.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/filter.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/interval_index_file.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/interval_index_file_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/seqmapping.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/seqmapping_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/wiggle.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/wiggle_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx copying lib/bx/bitset_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi copying lib/bx/bbi/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi copying lib/bx/bbi/bigwig_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif copying lib/bx/motif/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif copying lib/bx/motif/pwm_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif copying lib/bx/motif/pwm.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/seq_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/fasta_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/qdna_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/twobit_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/nib_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/twobit.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/fasta.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/core.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/nib.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/qdna.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq copying lib/bx/seq/seq.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/tabular copying lib/bx/tabular/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/tabular copying lib/bx/tabular/io.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/tabular creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals copying lib/bx/intervals/cluster_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals copying lib/bx/intervals/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals copying lib/bx/intervals/io.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals copying lib/bx/intervals/intersection_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals copying lib/bx/intervals/random_intervals.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intseq copying lib/bx/intseq/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intseq creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align copying lib/bx/align/axt.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align copying lib/bx/align/epo.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align copying lib/bx/align/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align copying lib/bx/align/lav.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align copying lib/bx/align/maf.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align copying lib/bx/align/maf_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align copying lib/bx/align/lav_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align copying lib/bx/align/score.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align copying lib/bx/align/score_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align copying lib/bx/align/core.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align copying lib/bx/align/epo_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/cookbook copying lib/bx/cookbook/argparse.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/cookbook copying lib/bx/cookbook/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/cookbook copying lib/bx/cookbook/progress_bar.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/cookbook copying lib/bx/cookbook/doc_optparse.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/cookbook copying lib/bx/cookbook/attribute.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/cookbook creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/binary_file.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/seekbzip2.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/readlengths.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/cdb.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/cdb_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/filecache.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/seeklzop.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/seekbzip2_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/seeklzop_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/bgzf_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc copying lib/bx/misc/filecache_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/arrays copying lib/bx/arrays/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/arrays copying lib/bx/arrays/array_tree_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/arrays creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/phylo copying lib/bx/phylo/phast.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/phylo copying lib/bx/phylo/newick_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/phylo copying lib/bx/phylo/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/phylo copying lib/bx/phylo/phast_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/phylo copying lib/bx/phylo/newick.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/phylo creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm copying lib/bx/pwm/pwm_score_maf.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm copying lib/bx/pwm/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm copying lib/bx/pwm/position_weight_matrix.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm copying lib/bx/pwm/pwm_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm copying lib/bx/pwm/maf_select_motifs.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm copying lib/bx/pwm/pwm_score_positions.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/logo copying lib/bx/motif/logo/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/logo creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/io copying lib/bx/motif/io/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/io copying lib/bx/motif/io/transfac.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/io copying lib/bx/motif/io/transfac_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/io creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/complement.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/quicksect.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/intersect.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/merge.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/coverage.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/join.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/subtract.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/base_coverage.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/find_clusters.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/concat.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask copying lib/bx/align/sitemask/quality.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask copying lib/bx/align/sitemask/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask copying lib/bx/align/sitemask/core.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask copying lib/bx/align/sitemask/cpg.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask creating build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/tools copying lib/bx/align/tools/chop.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/tools copying lib/bx/align/tools/__init__.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/tools copying lib/bx/align/tools/fuse.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/tools copying lib/bx/align/tools/tile.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/tools copying lib/bx/align/tools/thread.py -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/tools copying lib/bx/motif/logo/template.ps -> build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/logo running build_ext skipping 'lib/bx/bitset.c' Cython extension (up-to-date) skipping 'lib/bx/intervals/intersection.c' Cython extension (up-to-date) skipping 'lib/bx/align/_core.c' Cython extension (up-to-date) skipping 'lib/bx/seq/_nib.c' Cython extension (up-to-date) skipping 'lib/bx/seq/_twobit.c' Cython extension (up-to-date) skipping 'lib/bx/_seqmapping.c' Cython extension (up-to-date) skipping 'lib/bx/misc/bgzf.c' Cython extension (up-to-date) skipping 'lib/bx/intervals/cluster.c' Cython extension (up-to-date) skipping 'lib/bx/pwm/_position_weight_matrix.c' Cython extension (up-to-date) skipping 'lib/bx/motif/_pwm.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/array_tree.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bpt_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/cirtree_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bbi_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bigwig_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bigbed_file.c' Cython extension (up-to-date) skipping 'lib/bx/align/_epo.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/bed.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/wiggle.c' Cython extension (up-to-date) skipping 'lib/bx/align/sitemask/_cpg.c' Cython extension (up-to-date) skipping 'lib/bx/intseq/ngramcount.c' Cython extension (up-to-date) skipping 'lib/bx/misc/_seekbzip2.c' Cython extension (up-to-date) building 'bx.bitset' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39 creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/kent cc -Wno-unused-result -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/python3.9 -c lib/bx/bitset.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bitset.o cc -Wno-unused-result -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/python3.9 -c src/binBits.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/binBits.o cc -Wno-unused-result -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/python3.9 -c src/kent/bits.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/kent/bits.o cc -Wno-unused-result -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/python3.9 -c src/kent/common.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/kent/common.o cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bitset.o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/binBits.o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/kent/bits.o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/kent/common.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bitset.cpython-39.so building 'bx.intervals.intersection' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/intervals cc -Wno-unused-result -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/python3.9 -c lib/bx/intervals/intersection.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/intervals/intersection.o lib/bx/intervals/intersection.c:4089:5: warning: code will never be executed [-Wunreachable-code] PyErr_SetString(PyExc_ZeroDivisionError, "float division"); ^~~~~~~~~~~~~~~ lib/bx/intervals/intersection.c:15095:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/intervals/intersection.c:527:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/intervals/intersection.c:15106:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/intervals/intersection.c:527:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/intervals/intersection.c:15305:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/intervals/intersection.c:527:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/intervals/intersection.c:15316:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/intervals/intersection.c:527:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ 5 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/intervals/intersection.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/intersection.cpython-39.so building 'bx.align._core' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/align cc -Wno-unused-result -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/python3.9 -c lib/bx/align/_core.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/align/_core.o cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/align/_core.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/_core.cpython-39.so building 'bx.seq._nib' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/seq cc -Wno-unused-result -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/python3.9 -c lib/bx/seq/_nib.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/seq/_nib.o cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/seq/_nib.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/_nib.cpython-39.so building 'bx.seq._twobit' extension cc -Wno-unused-result -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/python3.9 -c lib/bx/seq/_twobit.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/seq/_twobit.o lib/bx/seq/_twobit.c:5616:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/seq/_twobit.c:527:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/seq/_twobit.c:5627:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/seq/_twobit.c:527:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ 2 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/seq/_twobit.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/_twobit.cpython-39.so building 'bx._seqmapping' extension cc -Wno-unused-result -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/python3.9 -c lib/bx/_seqmapping.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/_seqmapping.o lib/bx/_seqmapping.c:3590:15: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 54, __pyx_L1_error) ^ /usr/local/include/python3.9/abstract.h:353:1: note: 'PyObject_AsWriteBuffer' has been explicitly marked deprecated here Py_DEPRECATED(3.0) ^ /usr/local/include/python3.9/pyport.h:508:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ lib/bx/_seqmapping.c:3850:15: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_7 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 77, __pyx_L1_error) ^ /usr/local/include/python3.9/abstract.h:353:1: note: 'PyObject_AsWriteBuffer' has been explicitly marked deprecated here Py_DEPRECATED(3.0) ^ /usr/local/include/python3.9/pyport.h:508:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ lib/bx/_seqmapping.c:5288:15: warning: 'PyObject_AsReadBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_1 = PyObject_AsReadBuffer(__pyx_v_src, ((void const **)(&__pyx_v_s_buf)), (&__pyx_v_s_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 134, __pyx_L1_error) ^ /usr/local/include/python3.9/abstract.h:342:1: note: 'PyObject_AsReadBuffer' has been explicitly marked deprecated here Py_DEPRECATED(3.0) ^ /usr/local/include/python3.9/pyport.h:508:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ lib/bx/_seqmapping.c:5368:15: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 139, __pyx_L1_error) ^ /usr/local/include/python3.9/abstract.h:353:1: note: 'PyObject_AsWriteBuffer' has been explicitly marked deprecated here Py_DEPRECATED(3.0) ^ /usr/local/include/python3.9/pyport.h:508:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ lib/bx/_seqmapping.c:10160:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/_seqmapping.c:527:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/_seqmapping.c:10171:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/_seqmapping.c:527:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ 6 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/_seqmapping.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/_seqmapping.cpython-39.so building 'bx.misc.bgzf' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/misc creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/samtools cc -Wno-unused-result -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/python3.9 -c lib/bx/misc/bgzf.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/misc/bgzf.o cc -Wno-unused-result -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/python3.9 -c src/samtools/bgzf.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/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] 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] buffer[9] = OS_UNKNOWN; ~ ^~~~~~~~~~ src/samtools/bgzf.c:422:40: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 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] if (count != sizeof(header)) { ~~~~~ ^ ~~~~~~~~~~~~~~ 4 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/misc/bgzf.o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/samtools/bgzf.o -L/usr/local/lib -lz -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/bgzf.cpython-39.so building 'bx.intervals.cluster' extension cc -Wno-unused-result -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/python3.9 -c lib/bx/intervals/cluster.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/intervals/cluster.o cc -Wno-unused-result -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/python3.9 -c src/cluster.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/cluster.o cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/intervals/cluster.o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/cluster.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/cluster.cpython-39.so building 'bx.pwm._position_weight_matrix' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/pwm cc -Wno-unused-result -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/python3.9 -c lib/bx/pwm/_position_weight_matrix.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/pwm/_position_weight_matrix.o cc -Wno-unused-result -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/python3.9 -c src/pwm_utils.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/pwm_utils.o src/pwm_utils.c:11:27: warning: implicitly declaring library function 'strlen' with type 'unsigned long (const char *)' [-Wimplicit-function-declaration] int string_size = strlen(argv[1]); ^ src/pwm_utils.c:11:27: note: include the header or explicitly provide a declaration for 'strlen' src/pwm_utils.c:12:29: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (strlen(argv[2]) != string_size) { ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~ 2 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/pwm/_position_weight_matrix.o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/pwm_utils.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm/_position_weight_matrix.cpython-39.so building 'bx.motif._pwm' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/motif cc -Wno-unused-result -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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/motif/_pwm.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/motif/_pwm.o In file included from lib/bx/motif/_pwm.c:1205: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.9/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] #warning "Using deprecated NumPy API, disable it with " \ ^ 1 warning generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/motif/_pwm.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/_pwm.cpython-39.so building 'bx.arrays.array_tree' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/arrays cc -Wno-unused-result -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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/arrays/array_tree.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/arrays/array_tree.o In file included from lib/bx/arrays/array_tree.c:1214: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.9/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] #warning "Using deprecated NumPy API, disable it with " \ ^ 1 warning generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/arrays/array_tree.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/arrays/array_tree.cpython-39.so building 'bx.bbi.bpt_file' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bbi cc -Wno-unused-result -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/python3.9 -c lib/bx/bbi/bpt_file.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bbi/bpt_file.o cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bbi/bpt_file.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/bpt_file.cpython-39.so building 'bx.bbi.cirtree_file' extension cc -Wno-unused-result -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/python3.9 -c lib/bx/bbi/cirtree_file.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bbi/cirtree_file.o cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bbi/cirtree_file.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/cirtree_file.cpython-39.so building 'bx.bbi.bbi_file' extension cc -Wno-unused-result -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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/bbi/bbi_file.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bbi/bbi_file.o In file included from lib/bx/bbi/bbi_file.c:1214: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.9/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] #warning "Using deprecated NumPy API, disable it with " \ ^ lib/bx/bbi/bbi_file.c:24627:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/bbi/bbi_file.c:536:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/bbi/bbi_file.c:24638:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/bbi/bbi_file.c:536:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/bbi/bbi_file.c:24759:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/bbi/bbi_file.c:536:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/bbi/bbi_file.c:24770:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/bbi/bbi_file.c:536:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/bbi/bbi_file.c:24941:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/bbi/bbi_file.c:536:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/bbi/bbi_file.c:24947:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/bbi/bbi_file.c:536:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ 7 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bbi/bbi_file.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/bbi_file.cpython-39.so building 'bx.bbi.bigwig_file' extension cc -Wno-unused-result -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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/bbi/bigwig_file.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bbi/bigwig_file.o In file included from lib/bx/bbi/bigwig_file.c:1214: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.9/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] #warning "Using deprecated NumPy API, disable it with " \ ^ lib/bx/bbi/bigwig_file.c:6507:29: warning: comparison of integers of different signs: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' (aka 'unsigned int') [-Wsign-compare] __pyx_t_11 = (__pyx_v_s < __pyx_v_self->start); ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~ lib/bx/bbi/bigwig_file.c:6536:29: warning: comparison of integers of different signs: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' (aka 'unsigned int') [-Wsign-compare] __pyx_t_11 = (__pyx_v_e > __pyx_v_self->end); ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~ lib/bx/bbi/bigwig_file.c:8788:76: warning: comparison of integers of different signs: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' (aka 'unsigned int') [-Wsign-compare] 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 -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bbi/bigwig_file.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/bigwig_file.cpython-39.so building 'bx.bbi.bigbed_file' extension cc -Wno-unused-result -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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/bbi/bigbed_file.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bbi/bigbed_file.o In file included from lib/bx/bbi/bigbed_file.c:1214: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.9/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] #warning "Using deprecated NumPy API, disable it with " \ ^ 1 warning generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/bbi/bigbed_file.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/bigbed_file.cpython-39.so building 'bx.align._epo' extension cc -Wno-unused-result -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/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/align/_epo.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/align/_epo.o In file included from lib/bx/align/_epo.c:1214: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.9/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] #warning "Using deprecated NumPy API, disable it with " \ ^ lib/bx/align/_epo.c:8885:236: warning: comparison of integers of different signs: '__pyx_t_5numpy_uint64_t' (aka 'unsigned long') and 'Py_ssize_t' (aka 'long') [-Wsign-compare] __pyx_t_5 = ((*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_uint64_t *, __pyx_pybuffernd_elements.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_elements.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_elements.diminfo[1].strides)) <= __pyx_v_cen); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~ lib/bx/align/_epo.c:14585:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/align/_epo.c:536:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/align/_epo.c:14596:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/align/_epo.c:536:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ 4 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/align/_epo.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/_epo.cpython-39.so building 'bx.arrays.bed' extension cc -Wno-unused-result -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/python3.9 -c lib/bx/arrays/bed.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/arrays/bed.o cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/arrays/bed.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/arrays/bed.cpython-39.so building 'bx.arrays.wiggle' extension cc -Wno-unused-result -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/python3.9 -c lib/bx/arrays/wiggle.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/arrays/wiggle.o lib/bx/arrays/wiggle.c:7796:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/arrays/wiggle.c:526:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ lib/bx/arrays/wiggle.c:7807:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ lib/bx/arrays/wiggle.c:526:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) ^ 2 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/arrays/wiggle.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/arrays/wiggle.cpython-39.so building 'bx.align.sitemask._cpg' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/align/sitemask cc -Wno-unused-result -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/python3.9 -c lib/bx/align/sitemask/_cpg.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/align/sitemask/_cpg.o cc -Wno-unused-result -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/python3.9 -c lib/bx/align/sitemask/find_cpg.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/align/sitemask/find_cpg.o cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/align/sitemask/_cpg.o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/align/sitemask/find_cpg.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask/_cpg.cpython-39.so building 'bx.intseq.ngramcount' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/intseq cc -Wno-unused-result -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/python3.9 -c lib/bx/intseq/ngramcount.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/intseq/ngramcount.o cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/intseq/ngramcount.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intseq/ngramcount.cpython-39.so building 'bx.misc._seekbzip2' extension creating build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/bunzip cc -Wno-unused-result -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/python3.9 -c lib/bx/misc/_seekbzip2.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/misc/_seekbzip2.o cc -Wno-unused-result -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/python3.9 -c src/bunzip/micro-bunzip.c -o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/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] 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] while (bd->inbufBitCountmaxLen) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ src/bunzip/micro-bunzip.c:400:13: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 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] bd->inbuf=inbuf; ^~~~~~ 5 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/lib/bx/misc/_seekbzip2.o build/temp.freebsd-13.2-RELEASE-p10-amd64-cpython-39/src/bunzip/micro-bunzip.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/_seekbzip2.cpython-39.so running build_scripts creating build/scripts-3.9 copying and adjusting scripts/wiggle_to_binned_array.py -> build/scripts-3.9 copying and adjusting scripts/maf_col_counts.py -> build/scripts-3.9 copying and adjusting scripts/table_add_column.py -> build/scripts-3.9 copying and adjusting scripts/bed_rand_intersect.py -> build/scripts-3.9 copying and adjusting scripts/nib_intervals_to_fasta.py -> build/scripts-3.9 copying and adjusting scripts/bnMapper.py -> build/scripts-3.9 copying and adjusting scripts/bed_merge_overlapping.py -> build/scripts-3.9 copying and adjusting scripts/wiggle_to_array_tree.py -> build/scripts-3.9 copying and adjusting scripts/bed_bigwig_profile.py -> build/scripts-3.9 copying and adjusting scripts/wiggle_to_simple.py -> build/scripts-3.9 copying and adjusting scripts/maf_chunk.py -> build/scripts-3.9 copying and adjusting scripts/maf_col_counts_all.py -> build/scripts-3.9 copying and adjusting scripts/aggregate_scores_in_intervals.py -> build/scripts-3.9 copying and adjusting scripts/wiggle_to_chr_binned_array.py -> build/scripts-3.9 copying and adjusting scripts/maf_truncate.py -> build/scripts-3.9 copying and adjusting scripts/axt_to_fasta.py -> build/scripts-3.9 copying and adjusting scripts/maf_extract_chrom_ranges.py -> build/scripts-3.9 copying and adjusting scripts/maf_count.py -> build/scripts-3.9 copying and adjusting scripts/maf_region_coverage_by_src.py -> build/scripts-3.9 copying and adjusting scripts/gene_fourfold_sites.py -> build/scripts-3.9 copying and adjusting scripts/interval_join.py -> build/scripts-3.9 copying and adjusting scripts/mask_quality.py -> build/scripts-3.9 copying and adjusting scripts/maf_select.py -> build/scripts-3.9 copying and adjusting scripts/nib_length.py -> build/scripts-3.9 copying and adjusting scripts/bed_count_by_interval.py -> build/scripts-3.9 copying and adjusting scripts/maf_gap_frequency.py -> build/scripts-3.9 copying and adjusting scripts/maf_tile_2bit.py -> build/scripts-3.9 copying and adjusting scripts/maf_tile_2.py -> build/scripts-3.9 copying and adjusting scripts/maf_mask_cpg.py -> build/scripts-3.9 copying and adjusting scripts/div_snp_table_chr.py -> build/scripts-3.9 copying and adjusting scripts/maf_chop.py -> build/scripts-3.9 copying and adjusting scripts/lav_to_maf.py -> build/scripts-3.9 copying and adjusting scripts/bed_coverage.py -> build/scripts-3.9 copying and adjusting scripts/bed_diff_basewise_summary.py -> build/scripts-3.9 copying and adjusting scripts/maf_mapping_word_frequency.py -> build/scripts-3.9 copying and adjusting scripts/maf_build_index.py -> build/scripts-3.9 copying and adjusting scripts/tfloc_summary.py -> build/scripts-3.9 copying and adjusting scripts/bed_intersect.py -> build/scripts-3.9 copying and adjusting scripts/get_scores_in_intervals.py -> build/scripts-3.9 copying and adjusting scripts/bed_build_windows.py -> build/scripts-3.9 copying and adjusting scripts/maf_print_chroms.py -> build/scripts-3.9 copying and adjusting scripts/maf_div_sites.py -> build/scripts-3.9 copying and adjusting scripts/lav_to_axt.py -> build/scripts-3.9 copying and adjusting scripts/maf_to_concat_fasta.py -> build/scripts-3.9 copying and adjusting scripts/prefix_lines.py -> build/scripts-3.9 copying and adjusting scripts/maf_mean_length_ungapped_piece.py -> build/scripts-3.9 copying and adjusting scripts/pretty_table.py -> build/scripts-3.9 copying and adjusting scripts/bed_extend_to.py -> build/scripts-3.9 copying and adjusting scripts/bed_subtract_basewise.py -> build/scripts-3.9 copying and adjusting scripts/maf_to_axt.py -> build/scripts-3.9 copying and adjusting scripts/maf_word_frequency.py -> build/scripts-3.9 copying and adjusting scripts/maf_covered_regions.py -> build/scripts-3.9 copying and adjusting scripts/line_select.py -> build/scripts-3.9 copying and adjusting scripts/maf_to_fasta.py -> build/scripts-3.9 copying and adjusting scripts/maf_species_in_all_files.py -> build/scripts-3.9 copying and adjusting scripts/maf_thread_for_species.py -> build/scripts-3.9 copying and adjusting scripts/table_filter.py -> build/scripts-3.9 copying and adjusting scripts/bed_count_overlapping.py -> build/scripts-3.9 copying and adjusting scripts/interval_count_intersections.py -> build/scripts-3.9 copying and adjusting scripts/maf_percent_identity.py -> build/scripts-3.9 copying and adjusting scripts/int_seqs_to_char_strings.py -> build/scripts-3.9 copying and adjusting scripts/bed_complement.py -> build/scripts-3.9 copying and adjusting scripts/maf_gc_content.py -> build/scripts-3.9 copying and adjusting scripts/maf_interval_alignibility.py -> build/scripts-3.9 copying and adjusting scripts/maf_print_scores.py -> build/scripts-3.9 copying and adjusting scripts/maf_to_int_seqs.py -> build/scripts-3.9 copying and adjusting scripts/nib_chrom_intervals_to_fasta.py -> build/scripts-3.9 copying and adjusting scripts/maf_split_by_src.py -> build/scripts-3.9 copying and adjusting scripts/align_print_template.py -> build/scripts-3.9 copying and adjusting scripts/maf_shuffle_columns.py -> build/scripts-3.9 copying and adjusting scripts/mMK_bitset.py -> build/scripts-3.9 copying and adjusting scripts/maf_translate_chars.py -> build/scripts-3.9 copying and adjusting scripts/maf_percent_columns_matching.py -> build/scripts-3.9 copying and adjusting scripts/maf_filter_max_wc.py -> build/scripts-3.9 copying and adjusting scripts/bed_coverage_by_interval.py -> build/scripts-3.9 copying and adjusting scripts/bed_intersect_basewise.py -> build/scripts-3.9 copying and adjusting scripts/one_field_per_line.py -> build/scripts-3.9 copying and adjusting scripts/maf_drop_overlapping.py -> build/scripts-3.9 copying and adjusting scripts/find_in_sorted_file.py -> build/scripts-3.9 copying and adjusting scripts/qv_to_bqv.py -> build/scripts-3.9 copying and adjusting scripts/axt_to_maf.py -> build/scripts-3.9 copying and adjusting scripts/axt_extract_ranges.py -> build/scripts-3.9 copying and adjusting scripts/maf_tile.py -> build/scripts-3.9 copying and adjusting scripts/maf_covered_ranges.py -> build/scripts-3.9 copying and adjusting scripts/maf_filter.py -> build/scripts-3.9 copying and adjusting scripts/axt_to_lav.py -> build/scripts-3.9 copying and adjusting scripts/maf_extract_ranges.py -> build/scripts-3.9 copying and adjusting scripts/maf_extract_ranges_indexed.py -> build/scripts-3.9 copying and adjusting scripts/maf_randomize.py -> build/scripts-3.9 copying and adjusting scripts/ucsc_gene_table_to_intervals.py -> build/scripts-3.9 copying and adjusting scripts/out_to_chain.py -> build/scripts-3.9 copying and adjusting scripts/random_lines.py -> build/scripts-3.9 copying and adjusting scripts/maf_limit_to_species.py -> build/scripts-3.9 copying and adjusting scripts/lzop_build_offset_table.py -> build/scripts-3.9 changing mode of build/scripts-3.9/wiggle_to_binned_array.py from 644 to 755 changing mode of build/scripts-3.9/maf_col_counts.py from 644 to 755 changing mode of build/scripts-3.9/table_add_column.py from 644 to 755 changing mode of build/scripts-3.9/bed_rand_intersect.py from 644 to 755 changing mode of build/scripts-3.9/nib_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.9/bnMapper.py from 644 to 755 changing mode of build/scripts-3.9/bed_merge_overlapping.py from 644 to 755 changing mode of build/scripts-3.9/wiggle_to_array_tree.py from 644 to 755 changing mode of build/scripts-3.9/bed_bigwig_profile.py from 644 to 755 changing mode of build/scripts-3.9/wiggle_to_simple.py from 644 to 755 changing mode of build/scripts-3.9/maf_chunk.py from 644 to 755 changing mode of build/scripts-3.9/maf_col_counts_all.py from 644 to 755 changing mode of build/scripts-3.9/aggregate_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.9/wiggle_to_chr_binned_array.py from 644 to 755 changing mode of build/scripts-3.9/maf_truncate.py from 644 to 755 changing mode of build/scripts-3.9/axt_to_fasta.py from 644 to 755 changing mode of build/scripts-3.9/maf_extract_chrom_ranges.py from 644 to 755 changing mode of build/scripts-3.9/maf_count.py from 644 to 755 changing mode of build/scripts-3.9/maf_region_coverage_by_src.py from 644 to 755 changing mode of build/scripts-3.9/gene_fourfold_sites.py from 644 to 755 changing mode of build/scripts-3.9/interval_join.py from 644 to 755 changing mode of build/scripts-3.9/mask_quality.py from 644 to 755 changing mode of build/scripts-3.9/maf_select.py from 644 to 755 changing mode of build/scripts-3.9/nib_length.py from 644 to 755 changing mode of build/scripts-3.9/bed_count_by_interval.py from 644 to 755 changing mode of build/scripts-3.9/maf_gap_frequency.py from 644 to 755 changing mode of build/scripts-3.9/maf_tile_2bit.py from 644 to 755 changing mode of build/scripts-3.9/maf_tile_2.py from 644 to 755 changing mode of build/scripts-3.9/maf_mask_cpg.py from 644 to 755 changing mode of build/scripts-3.9/div_snp_table_chr.py from 644 to 755 changing mode of build/scripts-3.9/maf_chop.py from 644 to 755 changing mode of build/scripts-3.9/lav_to_maf.py from 644 to 755 changing mode of build/scripts-3.9/bed_coverage.py from 644 to 755 changing mode of build/scripts-3.9/bed_diff_basewise_summary.py from 644 to 755 changing mode of build/scripts-3.9/maf_mapping_word_frequency.py from 644 to 755 changing mode of build/scripts-3.9/maf_build_index.py from 644 to 755 changing mode of build/scripts-3.9/tfloc_summary.py from 644 to 755 changing mode of build/scripts-3.9/bed_intersect.py from 644 to 755 changing mode of build/scripts-3.9/get_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.9/bed_build_windows.py from 644 to 755 changing mode of build/scripts-3.9/maf_print_chroms.py from 644 to 755 changing mode of build/scripts-3.9/maf_div_sites.py from 644 to 755 changing mode of build/scripts-3.9/lav_to_axt.py from 644 to 755 changing mode of build/scripts-3.9/maf_to_concat_fasta.py from 644 to 755 changing mode of build/scripts-3.9/prefix_lines.py from 644 to 755 changing mode of build/scripts-3.9/maf_mean_length_ungapped_piece.py from 644 to 755 changing mode of build/scripts-3.9/pretty_table.py from 644 to 755 changing mode of build/scripts-3.9/bed_extend_to.py from 644 to 755 changing mode of build/scripts-3.9/bed_subtract_basewise.py from 644 to 755 changing mode of build/scripts-3.9/maf_to_axt.py from 644 to 755 changing mode of build/scripts-3.9/maf_word_frequency.py from 644 to 755 changing mode of build/scripts-3.9/maf_covered_regions.py from 644 to 755 changing mode of build/scripts-3.9/line_select.py from 644 to 755 changing mode of build/scripts-3.9/maf_to_fasta.py from 644 to 755 changing mode of build/scripts-3.9/maf_species_in_all_files.py from 644 to 755 changing mode of build/scripts-3.9/maf_thread_for_species.py from 644 to 755 changing mode of build/scripts-3.9/table_filter.py from 644 to 755 changing mode of build/scripts-3.9/bed_count_overlapping.py from 644 to 755 changing mode of build/scripts-3.9/interval_count_intersections.py from 644 to 755 changing mode of build/scripts-3.9/maf_percent_identity.py from 644 to 755 changing mode of build/scripts-3.9/int_seqs_to_char_strings.py from 644 to 755 changing mode of build/scripts-3.9/bed_complement.py from 644 to 755 changing mode of build/scripts-3.9/maf_gc_content.py from 644 to 755 changing mode of build/scripts-3.9/maf_interval_alignibility.py from 644 to 755 changing mode of build/scripts-3.9/maf_print_scores.py from 644 to 755 changing mode of build/scripts-3.9/maf_to_int_seqs.py from 644 to 755 changing mode of build/scripts-3.9/nib_chrom_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.9/maf_split_by_src.py from 644 to 755 changing mode of build/scripts-3.9/align_print_template.py from 644 to 755 changing mode of build/scripts-3.9/maf_shuffle_columns.py from 644 to 755 changing mode of build/scripts-3.9/mMK_bitset.py from 644 to 755 changing mode of build/scripts-3.9/maf_translate_chars.py from 644 to 755 changing mode of build/scripts-3.9/maf_percent_columns_matching.py from 644 to 755 changing mode of build/scripts-3.9/maf_filter_max_wc.py from 644 to 755 changing mode of build/scripts-3.9/bed_coverage_by_interval.py from 644 to 755 changing mode of build/scripts-3.9/bed_intersect_basewise.py from 644 to 755 changing mode of build/scripts-3.9/one_field_per_line.py from 644 to 755 changing mode of build/scripts-3.9/maf_drop_overlapping.py from 644 to 755 changing mode of build/scripts-3.9/find_in_sorted_file.py from 644 to 755 changing mode of build/scripts-3.9/qv_to_bqv.py from 644 to 755 changing mode of build/scripts-3.9/axt_to_maf.py from 644 to 755 changing mode of build/scripts-3.9/axt_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.9/maf_tile.py from 644 to 755 changing mode of build/scripts-3.9/maf_covered_ranges.py from 644 to 755 changing mode of build/scripts-3.9/maf_filter.py from 644 to 755 changing mode of build/scripts-3.9/axt_to_lav.py from 644 to 755 changing mode of build/scripts-3.9/maf_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.9/maf_extract_ranges_indexed.py from 644 to 755 changing mode of build/scripts-3.9/maf_randomize.py from 644 to 755 changing mode of build/scripts-3.9/ucsc_gene_table_to_intervals.py from 644 to 755 changing mode of build/scripts-3.9/out_to_chain.py from 644 to 755 changing mode of build/scripts-3.9/random_lines.py from 644 to 755 changing mode of build/scripts-3.9/maf_limit_to_species.py from 644 to 755 changing mode of build/scripts-3.9/lzop_build_offset_table.py from 644 to 755 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-bx-python-0.11.0 depends on package: py39-numpy>=1.16,1<1.26,1 - found ===> py39-bx-python-0.11.0 depends on package: py39-setuptools>=63.1.0 - found ===> py39-bx-python-0.11.0 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py39-bx-python-0.11.0 ===> Generating temporary packing list running install /usr/local/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_ext skipping 'lib/bx/bitset.c' Cython extension (up-to-date) skipping 'lib/bx/intervals/intersection.c' Cython extension (up-to-date) skipping 'lib/bx/align/_core.c' Cython extension (up-to-date) skipping 'lib/bx/seq/_nib.c' Cython extension (up-to-date) skipping 'lib/bx/seq/_twobit.c' Cython extension (up-to-date) skipping 'lib/bx/_seqmapping.c' Cython extension (up-to-date) skipping 'lib/bx/misc/bgzf.c' Cython extension (up-to-date) skipping 'lib/bx/intervals/cluster.c' Cython extension (up-to-date) skipping 'lib/bx/pwm/_position_weight_matrix.c' Cython extension (up-to-date) skipping 'lib/bx/motif/_pwm.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/array_tree.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bpt_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/cirtree_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bbi_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bigwig_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bigbed_file.c' Cython extension (up-to-date) skipping 'lib/bx/align/_epo.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/bed.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/wiggle.c' Cython extension (up-to-date) skipping 'lib/bx/align/sitemask/_cpg.c' Cython extension (up-to-date) skipping 'lib/bx/intseq/ngramcount.c' Cython extension (up-to-date) skipping 'lib/bx/misc/_seekbzip2.c' Cython extension (up-to-date) running build_scripts running install_lib creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9 creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/psyco_full.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras/fpconst.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras/stats.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras/lrucache.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras/pyparsing.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras/pstat.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx_extras/fpconst_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bitset.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/bpt_file.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/bigwig_file.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/bigbed_file.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/bbi_file.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/cirtree_file.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bbi/bigwig_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/binned_array.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bitset_utils.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/_pwm.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/logo copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/logo/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/logo copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/logo/template.ps -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/logo copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/pwm_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/io/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/io/transfac.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/io/transfac_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/io copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/motif/pwm.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/seq_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/_twobit.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/fasta_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/_nib.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/qdna_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/twobit_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/nib_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/twobit.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/fasta.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/core.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/nib.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/qdna.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seq/seq.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/_seqmapping.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/binned_array_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/tabular copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/tabular/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/tabular copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/tabular/io.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/tabular copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/gene_reader.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bitset_builders.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/filter.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/interval_index_file.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations/complement.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations/quicksect.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations/intersect.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations/merge.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations/coverage.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations/join.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations/subtract.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations/base_coverage.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations/find_clusters.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/operations/concat.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/cluster_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/cluster.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/io.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/intersection_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/intersection.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intervals/random_intervals.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/interval_index_file_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intseq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intseq/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intseq copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/intseq/ngramcount.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intseq creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/axt.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask/_cpg.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask/quality.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask/sitemask_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask/core.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/sitemask/cpg.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/epo.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/_epo.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/lav.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/maf.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/maf_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/lav_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/tools/chop.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/tools/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/tools/fuse.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/tools/tile.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/tools/thread.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/score.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/score_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/core.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/_core.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/align/epo_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/cookbook copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/cookbook/argparse.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/cookbook copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/cookbook/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/cookbook copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/cookbook/progress_bar.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/cookbook copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/cookbook/doc_optparse.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/cookbook copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/cookbook/attribute.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/cookbook creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/bgzf.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/binary_file.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/seekbzip2.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/readlengths.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/cdb.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/cdb_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/filecache.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/seeklzop.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/_seekbzip2.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/seekbzip2_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/seeklzop_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/bgzf_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/misc/filecache_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/arrays copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/arrays/wiggle.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/arrays copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/arrays/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/arrays copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/arrays/array_tree_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/arrays copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/arrays/array_tree.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/arrays copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/arrays/bed.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/arrays copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seqmapping.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/phylo copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/phylo/phast.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/phylo copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/phylo/newick_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/phylo copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/phylo/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/phylo copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/phylo/phast_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/phylo copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/phylo/newick.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/phylo copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/seqmapping_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/wiggle.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx creating /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm/bed_score_aligned_string.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm/pwm_score_maf.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm/__init__.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm/position_weight_matrix.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm/pwm_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm/maf_select_motifs.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm/bed_score_aligned_pwm.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm/pwm_score_motifs.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm/_position_weight_matrix.cpython-39.so -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/pwm/pwm_score_positions.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/wiggle_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.freebsd-13.2-RELEASE-p10-amd64-cpython-39/bx/bitset_tests.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/psyco_full.py to psyco_full.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras/fpconst.py to fpconst.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras/stats.py to stats.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras/lrucache.py to lrucache.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras/pyparsing.py to pyparsing.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras/pstat.py to pstat.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_extras/fpconst_tests.py to fpconst_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bbi/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bbi/bigwig_tests.py to bigwig_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/binned_array.py to binned_array.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bitset_utils.py to bitset_utils.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/logo/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/pwm_tests.py to pwm_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/io/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/io/transfac.py to transfac.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/io/transfac_tests.py to transfac_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/motif/pwm.py to pwm.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/seq_tests.py to seq_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/fasta_tests.py to fasta_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/qdna_tests.py to qdna_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/twobit_tests.py to twobit_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/nib_tests.py to nib_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/twobit.py to twobit.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/fasta.py to fasta.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/core.py to core.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/nib.py to nib.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/qdna.py to qdna.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seq/seq.py to seq.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/binned_array_tests.py to binned_array_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/tabular/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/tabular/io.py to io.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/gene_reader.py to gene_reader.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bitset_builders.py to bitset_builders.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/filter.py to filter.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/interval_index_file.py to interval_index_file.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/complement.py to complement.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/quicksect.py to quicksect.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/intersect.py to intersect.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/merge.py to merge.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/coverage.py to coverage.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/join.py to join.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/subtract.py to subtract.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/base_coverage.py to base_coverage.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/find_clusters.py to find_clusters.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/concat.py to concat.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/cluster_tests.py to cluster_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/io.py to io.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/intersection_tests.py to intersection_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intervals/random_intervals.py to random_intervals.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/interval_index_file_tests.py to interval_index_file_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/intseq/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/axt.py to axt.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask/quality.py to quality.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask/sitemask_tests.py to sitemask_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask/core.py to core.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask/cpg.py to cpg.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/epo.py to epo.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/lav.py to lav.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/maf.py to maf.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/maf_tests.py to maf_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/lav_tests.py to lav_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/tools/chop.py to chop.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/tools/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/tools/fuse.py to fuse.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/tools/tile.py to tile.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/tools/thread.py to thread.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/score.py to score.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/score_tests.py to score_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/core.py to core.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/align/epo_tests.py to epo_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/cookbook/argparse.py to argparse.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/cookbook/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/cookbook/progress_bar.py to progress_bar.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/cookbook/doc_optparse.py to doc_optparse.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/cookbook/attribute.py to attribute.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/binary_file.py to binary_file.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/seekbzip2.py to seekbzip2.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/readlengths.py to readlengths.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/cdb.py to cdb.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/cdb_tests.py to cdb_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/filecache.py to filecache.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/seeklzop.py to seeklzop.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/seekbzip2_tests.py to seekbzip2_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/seeklzop_tests.py to seeklzop_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/bgzf_tests.py to bgzf_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/misc/filecache_tests.py to filecache_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/arrays/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/arrays/array_tree_tests.py to array_tree_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seqmapping.py to seqmapping.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/phylo/phast.py to phast.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/phylo/newick_tests.py to newick_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/phylo/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/phylo/phast_tests.py to phast_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/phylo/newick.py to newick.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/seqmapping_tests.py to seqmapping_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/wiggle.py to wiggle.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm/bed_score_aligned_string.py to bed_score_aligned_string.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm/pwm_score_maf.py to pwm_score_maf.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm/__init__.py to __init__.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm/position_weight_matrix.py to position_weight_matrix.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm/pwm_tests.py to pwm_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm/maf_select_motifs.py to maf_select_motifs.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm/bed_score_aligned_pwm.py to bed_score_aligned_pwm.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm/pwm_score_motifs.py to pwm_score_motifs.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/pwm/pwm_score_positions.py to pwm_score_positions.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/wiggle_tests.py to wiggle_tests.cpython-39.pyc byte-compiling /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx/bitset_tests.py to bitset_tests.cpython-39.pyc writing byte-compilation script '/tmp/tmpv7a44vbf.py' /usr/local/bin/python3.9 /tmp/tmpv7a44vbf.py removing /tmp/tmpv7a44vbf.py running install_egg_info 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_python.egg-info to /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/lib/python3.9/site-packages/bx_python-0.11.0-py3.9.egg-info running install_scripts copying build/scripts-3.9/wiggle_to_binned_array.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_col_counts.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/table_add_column.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_rand_intersect.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/nib_intervals_to_fasta.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bnMapper.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_merge_overlapping.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/wiggle_to_array_tree.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_bigwig_profile.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/wiggle_to_simple.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_chunk.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_col_counts_all.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/aggregate_scores_in_intervals.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/wiggle_to_chr_binned_array.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_truncate.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/axt_to_fasta.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_extract_chrom_ranges.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_count.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_region_coverage_by_src.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/gene_fourfold_sites.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/interval_join.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/mask_quality.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_select.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/nib_length.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_count_by_interval.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_gap_frequency.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_tile_2bit.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_tile_2.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_mask_cpg.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/div_snp_table_chr.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_chop.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/lav_to_maf.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_coverage.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_diff_basewise_summary.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_mapping_word_frequency.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_build_index.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/tfloc_summary.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_intersect.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/get_scores_in_intervals.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_build_windows.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_print_chroms.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_div_sites.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/lav_to_axt.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_to_concat_fasta.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/prefix_lines.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_mean_length_ungapped_piece.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/pretty_table.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_extend_to.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_subtract_basewise.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_to_axt.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_word_frequency.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_covered_regions.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/line_select.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_to_fasta.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_species_in_all_files.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_thread_for_species.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/table_filter.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_count_overlapping.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/interval_count_intersections.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_percent_identity.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/int_seqs_to_char_strings.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_complement.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_gc_content.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_interval_alignibility.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_print_scores.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_to_int_seqs.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/nib_chrom_intervals_to_fasta.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_split_by_src.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/align_print_template.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_shuffle_columns.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/mMK_bitset.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_translate_chars.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_percent_columns_matching.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_filter_max_wc.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_coverage_by_interval.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/bed_intersect_basewise.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/one_field_per_line.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_drop_overlapping.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/find_in_sorted_file.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/qv_to_bqv.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/axt_to_maf.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/axt_extract_ranges.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_tile.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_covered_ranges.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_filter.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/axt_to_lav.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_extract_ranges.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_extract_ranges_indexed.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_randomize.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/ucsc_gene_table_to_intervals.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/out_to_chain.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/random_lines.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/maf_limit_to_species.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin copying build/scripts-3.9/lzop_build_offset_table.py -> /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/wiggle_to_binned_array.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_col_counts.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/table_add_column.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_rand_intersect.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/nib_intervals_to_fasta.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bnMapper.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_merge_overlapping.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/wiggle_to_array_tree.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_bigwig_profile.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/wiggle_to_simple.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_chunk.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_col_counts_all.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/aggregate_scores_in_intervals.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/wiggle_to_chr_binned_array.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_truncate.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/axt_to_fasta.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_extract_chrom_ranges.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_count.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_region_coverage_by_src.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/gene_fourfold_sites.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/interval_join.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/mask_quality.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_select.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/nib_length.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_count_by_interval.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_gap_frequency.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_tile_2bit.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_tile_2.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_mask_cpg.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/div_snp_table_chr.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_chop.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/lav_to_maf.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_coverage.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_diff_basewise_summary.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_mapping_word_frequency.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_build_index.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/tfloc_summary.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_intersect.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/get_scores_in_intervals.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_build_windows.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_print_chroms.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_div_sites.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/lav_to_axt.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_to_concat_fasta.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/prefix_lines.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_mean_length_ungapped_piece.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/pretty_table.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_extend_to.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_subtract_basewise.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_to_axt.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_word_frequency.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_covered_regions.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/line_select.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_to_fasta.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_species_in_all_files.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_thread_for_species.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/table_filter.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_count_overlapping.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/interval_count_intersections.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_percent_identity.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/int_seqs_to_char_strings.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_complement.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_gc_content.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_interval_alignibility.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_print_scores.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_to_int_seqs.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/nib_chrom_intervals_to_fasta.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_split_by_src.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/align_print_template.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_shuffle_columns.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/mMK_bitset.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_translate_chars.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_percent_columns_matching.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_filter_max_wc.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_coverage_by_interval.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/bed_intersect_basewise.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/one_field_per_line.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_drop_overlapping.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/find_in_sorted_file.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/qv_to_bqv.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/axt_to_maf.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/axt_extract_ranges.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_tile.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_covered_ranges.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_filter.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/axt_to_lav.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_extract_ranges.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_extract_ranges_indexed.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_randomize.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/ucsc_gene_table_to_intervals.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/out_to_chain.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/random_lines.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/maf_limit_to_species.py to 755 changing mode of /wrkdirs/usr/ports/biology/py-bx-python/work-py39/stage/usr/local/bin/lzop_build_offset_table.py to 755 writing list of installed files to '/wrkdirs/usr/ports/biology/py-bx-python/work-py39/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-03-28T08:09:56+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=3fad843b18' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for py39-bx-python-0.11.0 ===> Building py39-bx-python-0.11.0 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py39-bx-python-0.11.0 build of biology/py-bx-python@py39 | py39-bx-python-0.11.0 ended at Thu Mar 28 08:11:58 GMT 2024 build time: 00:02:04