=>> Building biology/py-crossmap build started at Sun Mar 15 20:42:04 EDT 2026 port directory: /usr/ports/biology/py-crossmap package name: py311-crossmap-0.7.3_1 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 723 Mar 10 2025 /usr/ports/biology/py-crossmap/Makefile Ports top last git commit: 8c988f802ea2 Ports top unclean checkout: no Port dir last git commit: 06a08e69f3ac Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 11 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/11/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py311 MAKE_ARGS= FLAVOR=py311 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-crossmap/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-crossmap/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-crossmap/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-crossmap/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-crossmap/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-crossmap/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-crossmap/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-crossmap/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-crossmap/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-crossmap/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-crossmap/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-crossmap/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py311-crossmap" EXAMPLESDIR="share/examples/py311-crossmap" DATADIR="share/py311-crossmap" WWWDIR="www/py311-crossmap" ETCDIR="etc/py311-crossmap" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py311-crossmap DOCSDIR=/usr/local/share/doc/py311-crossmap EXAMPLESDIR=/usr/local/share/examples/py311-crossmap WWWDIR=/usr/local/www/py311-crossmap ETCDIR=/usr/local/etc/py311-crossmap --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-crossmap-0.7.3_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> py311-crossmap-0.7.3_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-crossmap-0.7.3_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-crossmap-0.7.3_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-crossmap-0.7.3_1 for building => SHA256 Checksum OK for crossmap-0.7.3.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-crossmap-0.7.3_1 for building ===> Extracting for py311-crossmap-0.7.3_1 => SHA256 Checksum OK for crossmap-0.7.3.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py311-crossmap-0.7.3_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-crossmap-0.7.3_1 depends on package: py311-nose>0.10.4 - not found ===> Installing existing package /packages/All/py311-nose-1.3.7_2.pkg [pkg.DaveG.ca] Installing py311-nose-1.3.7_2... [pkg.DaveG.ca] `-- Installing python311-3.11.15... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.15: .......... done [pkg.DaveG.ca] Extracting py311-nose-1.3.7_2: .......... done ===== Message from python311-3.11.15: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> py311-crossmap-0.7.3_1 depends on package: py311-nose>0.10.4 - found ===> Returning to build of py311-crossmap-0.7.3_1 ===> py311-crossmap-0.7.3_1 depends on package: py311-cython>=3.2.4 - not found ===> Installing existing package /packages/All/py311-cython-3.2.4.pkg [pkg.DaveG.ca] Installing py311-cython-3.2.4... [pkg.DaveG.ca] Extracting py311-cython-3.2.4: .......... done ===> py311-crossmap-0.7.3_1 depends on package: py311-cython>=3.2.4 - found ===> Returning to build of py311-crossmap-0.7.3_1 ===> py311-crossmap-0.7.3_1 depends on package: py311-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py311-setuptools-63.1.0_3.pkg [pkg.DaveG.ca] Installing py311-setuptools-63.1.0_3... [pkg.DaveG.ca] Extracting py311-setuptools-63.1.0_3: .......... done ===> py311-crossmap-0.7.3_1 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-crossmap-0.7.3_1 ===> py311-crossmap-0.7.3_1 depends on file: /usr/local/bin/python3.11 - found ===> py311-crossmap-0.7.3_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> py311-crossmap-0.7.3_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-crossmap-0.7.3_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py311-crossmap-0.7.3_1 running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py311-crossmap-0.7.3_1 running build running build_py creating build creating build/lib copying src/__init__.py -> build/lib creating build/lib/cmmodule copying src/cmmodule/mapgff.py -> build/lib/cmmodule copying src/cmmodule/bgrMerge.py -> build/lib/cmmodule copying src/cmmodule/annoGene.py -> build/lib/cmmodule copying src/cmmodule/__init__.py -> build/lib/cmmodule copying src/cmmodule/mapbam.py -> build/lib/cmmodule copying src/cmmodule/myutils.py -> build/lib/cmmodule copying src/cmmodule/meta_data.py -> build/lib/cmmodule copying src/cmmodule/mapwig.py -> build/lib/cmmodule copying src/cmmodule/mapgvcf.py -> build/lib/cmmodule copying src/cmmodule/mapregion.py -> build/lib/cmmodule copying src/cmmodule/ireader.py -> build/lib/cmmodule copying src/cmmodule/mapbed.py -> build/lib/cmmodule copying src/cmmodule/mapvcf.py -> build/lib/cmmodule copying src/cmmodule/BED.py -> build/lib/cmmodule copying src/cmmodule/utils.py -> build/lib/cmmodule copying src/cmmodule/wiggle.py -> build/lib/cmmodule copying src/cmmodule/wig_reader.py -> build/lib/cmmodule copying src/cmmodule/mapmaf.py -> build/lib/cmmodule copying src/cmmodule/sam_header.py -> build/lib/cmmodule running egg_info writing src/CrossMap.egg-info/PKG-INFO writing dependency_links to src/CrossMap.egg-info/dependency_links.txt writing entry points to src/CrossMap.egg-info/entry_points.txt writing requirements to src/CrossMap.egg-info/requires.txt writing top-level names to src/CrossMap.egg-info/top_level.txt reading manifest file 'src/CrossMap.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'src/CrossMap.egg-info/SOURCES.txt' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-crossmap-0.7.3_1 depends on package: py311-pysam>0 - not found ===> Installing existing package /packages/All/py311-pysam-0.23.0_1.pkg [pkg.DaveG.ca] Installing py311-pysam-0.23.0_1... [pkg.DaveG.ca] `-- Installing bcftools-1.22_1... [pkg.DaveG.ca] | `-- Installing bash-5.3.9... [pkg.DaveG.ca] | `-- Extracting bash-5.3.9: .......... done [pkg.DaveG.ca] | `-- Installing gsl-2.8... [pkg.DaveG.ca] | `-- Extracting gsl-2.8: .......... done [pkg.DaveG.ca] | `-- Installing htslib-1.22... [pkg.DaveG.ca] | | `-- Installing curl-8.17.0... [pkg.DaveG.ca] | | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | | `-- Installing libunistring-1.4.2... [pkg.DaveG.ca] | | | `-- Extracting libunistring-1.4.2: .......... done [pkg.DaveG.ca] | | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | | `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] | | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | | `-- Extracting curl-8.17.0: .......... done [pkg.DaveG.ca] | | `-- Installing libdeflate-1.25... [pkg.DaveG.ca] | | `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] | `-- Extracting htslib-1.22: .......... done [pkg.DaveG.ca] | `-- Installing perl5-5.42.1... [pkg.DaveG.ca] | `-- Extracting perl5-5.42.1: .......... done [pkg.DaveG.ca] `-- Extracting bcftools-1.22_1: .......... done [pkg.DaveG.ca] `-- Installing samtools-1.22... [pkg.DaveG.ca] `-- Extracting samtools-1.22: .......... done [pkg.DaveG.ca] Extracting py311-pysam-0.23.0_1: .......... done ===== Message from bash-5.3.9: -- bash requires fdescfs(5) mounted on /dev/fd If you have not done it yet, please do the following: mount -t fdescfs fdescfs /dev/fd To make it permanent, you need the following lines in /etc/fstab: fdescfs /dev/fd fdescfs rw,late 0 0 ===> py311-crossmap-0.7.3_1 depends on package: py311-pysam>0 - found ===> Returning to build of py311-crossmap-0.7.3_1 ===> py311-crossmap-0.7.3_1 depends on package: py311-bx-python>0 - not found ===> Installing existing package /packages/All/py311-bx-python-0.14.0.pkg [pkg.DaveG.ca] Installing py311-bx-python-0.14.0... [pkg.DaveG.ca] `-- Installing py311-numpy-1.26.4_12,1... [pkg.DaveG.ca] | `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] | `-- Extracting gcc14-14.2.0_4: .......... done create symlink for gcc14 create symlink for gcc14 (world) create symlink for g++14 create symlink for g++14 (world) create symlink for cpp14 create symlink for cpp14 (world) [pkg.DaveG.ca] | `-- Installing openblas-0.3.30,2... [pkg.DaveG.ca] | `-- Extracting openblas-0.3.30,2: .......... done [pkg.DaveG.ca] | `-- Installing suitesparse-umfpack-6.3.7... [pkg.DaveG.ca] | | `-- Installing suitesparse-amd-3.3.4... [pkg.DaveG.ca] | | `-- Installing suitesparse-config-7.12.2... [pkg.DaveG.ca] | | `-- Extracting suitesparse-config-7.12.2: .......... done [pkg.DaveG.ca] | | `-- Extracting suitesparse-amd-3.3.4: .......... done [pkg.DaveG.ca] | | `-- Installing suitesparse-camd-3.3.5... [pkg.DaveG.ca] | | `-- Extracting suitesparse-camd-3.3.5: .......... done [pkg.DaveG.ca] | | `-- Installing suitesparse-ccolamd-3.3.5... [pkg.DaveG.ca] | | `-- Extracting suitesparse-ccolamd-3.3.5: .......... done [pkg.DaveG.ca] | | `-- Installing suitesparse-cholmod-5.3.4... [pkg.DaveG.ca] | | `-- Installing suitesparse-colamd-3.3.5... [pkg.DaveG.ca] | | `-- Extracting suitesparse-colamd-3.3.5: .......... done [pkg.DaveG.ca] | | `-- Extracting suitesparse-cholmod-5.3.4: .......... done [pkg.DaveG.ca] | `-- Extracting suitesparse-umfpack-6.3.7: .......... done [pkg.DaveG.ca] `-- Extracting py311-numpy-1.26.4_12,1: .......... done [pkg.DaveG.ca] `-- Installing py311-pyparsing-3.3.2... [pkg.DaveG.ca] `-- Extracting py311-pyparsing-3.3.2: .......... done [pkg.DaveG.ca] Extracting py311-bx-python-0.14.0: .......... done ===== Message from gcc14-14.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> py311-crossmap-0.7.3_1 depends on package: py311-bx-python>0 - found ===> Returning to build of py311-crossmap-0.7.3_1 ===> py311-crossmap-0.7.3_1 depends on package: py311-pyBigWig>0 - not found ===> Installing existing package /packages/All/py311-pyBigWig-0.3.22_1.pkg [pkg.DaveG.ca] Installing py311-pyBigWig-0.3.22_1... [pkg.DaveG.ca] Extracting py311-pyBigWig-0.3.22_1: .......... done ===> py311-crossmap-0.7.3_1 depends on package: py311-pyBigWig>0 - found ===> Returning to build of py311-crossmap-0.7.3_1 ===> py311-crossmap-0.7.3_1 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py311-crossmap-0.7.3_1 ===> Generating temporary packing list running install /usr/local/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running egg_info writing src/CrossMap.egg-info/PKG-INFO writing dependency_links to src/CrossMap.egg-info/dependency_links.txt writing entry points to src/CrossMap.egg-info/entry_points.txt writing requirements to src/CrossMap.egg-info/requires.txt writing top-level names to src/CrossMap.egg-info/top_level.txt reading manifest file 'src/CrossMap.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'src/CrossMap.egg-info/SOURCES.txt' running install_lib creating /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11 creating /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages copying build/lib/__init__.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/mapgff.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/bgrMerge.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/annoGene.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/__init__.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/mapbam.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/myutils.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/meta_data.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/mapwig.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/mapgvcf.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/mapregion.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/ireader.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/mapbed.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/mapvcf.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/BED.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/utils.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/wiggle.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/wig_reader.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/mapmaf.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule copying build/lib/cmmodule/sam_header.py -> /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/mapgff.py to mapgff.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/bgrMerge.py to bgrMerge.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/annoGene.py to annoGene.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/mapbam.py to mapbam.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/myutils.py to myutils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/meta_data.py to meta_data.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/mapwig.py to mapwig.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/mapgvcf.py to mapgvcf.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/mapregion.py to mapregion.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/ireader.py to ireader.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/mapbed.py to mapbed.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/mapvcf.py to mapvcf.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/BED.py to BED.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/utils.py to utils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/wiggle.py to wiggle.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/wig_reader.py to wig_reader.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/mapmaf.py to mapmaf.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/cmmodule/sam_header.py to sam_header.cpython-311.pyc writing byte-compilation script '/tmp/tmp70bjbe_7.py' /usr/local/bin/python3.11 /tmp/tmp70bjbe_7.py removing /tmp/tmp70bjbe_7.py running install_egg_info Copying src/CrossMap.egg-info to /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/lib/python3.11/site-packages/CrossMap-0.7.3-py3.11.egg-info running install_scripts Installing CrossMap script to /wrkdirs/usr/ports/biology/py-crossmap/work-py311/stage/usr/local/bin writing list of installed files to '/wrkdirs/usr/ports/biology/py-crossmap/work-py311/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/CrossMap --> bin/CrossMap-3.11 Link: @bin/CrossMap --> bin/CrossMap-3.11 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-03-16T00:42:04+0000' 'PKG_NOTE_ports_top_git_hash=8c988f802ea2' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=06a08e69f3ac' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for py311-crossmap-0.7.3_1 ===> Building py311-crossmap-0.7.3_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-crossmap-0.7.3_1 build of biology/py-crossmap@py311 | py311-crossmap-0.7.3_1 ended at Sun Mar 15 20:42:57 EDT 2026 build time: 00:00:55