=>> Building biology/py-deeptools build started at Wed Mar 18 20:23:47 EDT 2026 port directory: /usr/ports/biology/py-deeptools package name: py311-deepTools-3.5.2_2 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 1052 Sep 22 04:12 /usr/ports/biology/py-deeptools/Makefile Ports top last git commit: 8c988f802ea2 Ports top unclean checkout: no Port dir last git commit: b304d8ab18ac Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 13 ---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/13/.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-deeptools/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-deeptools/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-deeptools/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-deeptools/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-deeptools/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-deeptools/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-deeptools/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-deeptools/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-deeptools/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-deeptools/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-deeptools/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-deeptools/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-deepTools" EXAMPLESDIR="share/examples/py311-deepTools" DATADIR="share/py311-deepTools" WWWDIR="www/py311-deepTools" ETCDIR="etc/py311-deepTools" --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-deepTools DOCSDIR=/usr/local/share/doc/py311-deepTools EXAMPLESDIR=/usr/local/share/examples/py311-deepTools WWWDIR=/usr/local/www/py311-deepTools ETCDIR=/usr/local/etc/py311-deepTools --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-deepTools-3.5.2_2 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-deepTools-3.5.2_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-deepTools-3.5.2_2 =========================================================================== =================================================== ===== 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-deepTools-3.5.2_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-deepTools-3.5.2_2 for building => SHA256 Checksum OK for deepTools-3.5.2.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-deepTools-3.5.2_2 for building ===> Extracting for py311-deepTools-3.5.2_2 => SHA256 Checksum OK for deepTools-3.5.2.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-deepTools-3.5.2_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-deepTools-3.5.2_2 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] `-- 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-setuptools-63.1.0_3: .......... 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-deepTools-3.5.2_2 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-deepTools-3.5.2_2 ===> py311-deepTools-3.5.2_2 depends on file: /usr/local/bin/python3.11 - found ===> py311-deepTools-3.5.2_2 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-deepTools-3.5.2_2 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-deepTools-3.5.2_2 =========================================================================== =================================================== ===== 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-deepTools-3.5.2_2 running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py311-deepTools-3.5.2_2 running build running build_py creating build creating build/lib creating build/lib/deeptools copying deeptools/sumCoveragePerBin.py -> build/lib/deeptools copying deeptools/countReadsPerBin.py -> build/lib/deeptools copying deeptools/plotEnrichment.py -> build/lib/deeptools copying deeptools/estimateReadFiltering.py -> build/lib/deeptools copying deeptools/computeMatrixOperations.py -> build/lib/deeptools copying deeptools/getScaleFactor.py -> build/lib/deeptools copying deeptools/alignmentSieve.py -> build/lib/deeptools copying deeptools/bigwigCompare.py -> build/lib/deeptools copying deeptools/getScorePerBigWigBin.py -> build/lib/deeptools copying deeptools/correlation.py -> build/lib/deeptools copying deeptools/parserCommon.py -> build/lib/deeptools copying deeptools/plotPCA.py -> build/lib/deeptools copying deeptools/__init__.py -> build/lib/deeptools copying deeptools/deepBlue.py -> build/lib/deeptools copying deeptools/correctGCBias.py -> build/lib/deeptools copying deeptools/bamPEFragmentSize.py -> build/lib/deeptools copying deeptools/correlation_heatmap.py -> build/lib/deeptools copying deeptools/writeBedGraph_bam_and_bw.py -> build/lib/deeptools copying deeptools/heatmapper_utilities.py -> build/lib/deeptools copying deeptools/multiBamSummary.py -> build/lib/deeptools copying deeptools/multiBigwigSummary.py -> build/lib/deeptools copying deeptools/plotHeatmap.py -> build/lib/deeptools copying deeptools/bamHandler.py -> build/lib/deeptools copying deeptools/bigwigAverage.py -> build/lib/deeptools copying deeptools/SES_scaleFactor.py -> build/lib/deeptools copying deeptools/misc.py -> build/lib/deeptools copying deeptools/getRatio.py -> build/lib/deeptools copying deeptools/mapReduce.py -> build/lib/deeptools copying deeptools/writeBedGraph.py -> build/lib/deeptools copying deeptools/utilities.py -> build/lib/deeptools copying deeptools/plotFingerprint.py -> build/lib/deeptools copying deeptools/cm.py -> build/lib/deeptools copying deeptools/plotCoverage.py -> build/lib/deeptools copying deeptools/getFragmentAndReadSize.py -> build/lib/deeptools copying deeptools/deeptools_list_tools.py -> build/lib/deeptools copying deeptools/bamCompare.py -> build/lib/deeptools copying deeptools/plotCorrelation.py -> build/lib/deeptools copying deeptools/computeMatrix.py -> build/lib/deeptools copying deeptools/plotProfile.py -> build/lib/deeptools copying deeptools/computeGCBias.py -> build/lib/deeptools copying deeptools/heatmapper.py -> build/lib/deeptools copying deeptools/bamCoverage.py -> build/lib/deeptools copying deeptools/_version.py -> build/lib/deeptools running egg_info writing deepTools.egg-info/PKG-INFO writing dependency_links to deepTools.egg-info/dependency_links.txt writing requirements to deepTools.egg-info/requires.txt writing top-level names to deepTools.egg-info/top_level.txt reading manifest file 'deepTools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'examples/*' warning: no previously-included files found matching 'deeptools/test/*' warning: no previously-included files found matching 'galaxy/*' warning: no previously-included files found matching 'gallery/*' adding license file 'LICENSE.txt' writing manifest file 'deepTools.egg-info/SOURCES.txt' running build_scripts creating build/scripts-3.11 copying and adjusting bin/bamCompare -> build/scripts-3.11 copying and adjusting bin/bamCoverage -> build/scripts-3.11 copying and adjusting bin/multiBamSummary -> build/scripts-3.11 copying and adjusting bin/plotHeatmap -> build/scripts-3.11 copying and adjusting bin/plotFingerprint -> build/scripts-3.11 copying and adjusting bin/estimateScaleFactor -> build/scripts-3.11 copying and adjusting bin/bamPEFragmentSize -> build/scripts-3.11 copying and adjusting bin/computeMatrix -> build/scripts-3.11 copying and adjusting bin/plotProfile -> build/scripts-3.11 copying and adjusting bin/computeGCBias -> build/scripts-3.11 copying and adjusting bin/correctGCBias -> build/scripts-3.11 copying and adjusting bin/multiBigwigSummary -> build/scripts-3.11 copying and adjusting bin/bigwigCompare -> build/scripts-3.11 copying and adjusting bin/plotCoverage -> build/scripts-3.11 copying and adjusting bin/plotPCA -> build/scripts-3.11 copying and adjusting bin/plotCorrelation -> build/scripts-3.11 copying and adjusting bin/plotEnrichment -> build/scripts-3.11 copying and adjusting bin/deeptools -> build/scripts-3.11 copying and adjusting bin/computeMatrixOperations -> build/scripts-3.11 copying and adjusting bin/estimateReadFiltering -> build/scripts-3.11 copying and adjusting bin/alignmentSieve -> build/scripts-3.11 copying and adjusting bin/bigwigAverage -> build/scripts-3.11 changing mode of build/scripts-3.11/bamCompare from 644 to 755 changing mode of build/scripts-3.11/bamCoverage from 644 to 755 changing mode of build/scripts-3.11/multiBamSummary from 644 to 755 changing mode of build/scripts-3.11/plotHeatmap from 644 to 755 changing mode of build/scripts-3.11/plotFingerprint from 644 to 755 changing mode of build/scripts-3.11/estimateScaleFactor from 644 to 755 changing mode of build/scripts-3.11/bamPEFragmentSize from 644 to 755 changing mode of build/scripts-3.11/computeMatrix from 644 to 755 changing mode of build/scripts-3.11/plotProfile from 644 to 755 changing mode of build/scripts-3.11/computeGCBias from 644 to 755 changing mode of build/scripts-3.11/correctGCBias from 644 to 755 changing mode of build/scripts-3.11/multiBigwigSummary from 644 to 755 changing mode of build/scripts-3.11/bigwigCompare from 644 to 755 changing mode of build/scripts-3.11/plotCoverage from 644 to 755 changing mode of build/scripts-3.11/plotPCA from 644 to 755 changing mode of build/scripts-3.11/plotCorrelation from 644 to 755 changing mode of build/scripts-3.11/plotEnrichment from 644 to 755 changing mode of build/scripts-3.11/deeptools from 644 to 755 changing mode of build/scripts-3.11/computeMatrixOperations from 644 to 755 changing mode of build/scripts-3.11/estimateReadFiltering from 644 to 755 changing mode of build/scripts-3.11/alignmentSieve from 644 to 755 changing mode of build/scripts-3.11/bigwigAverage from 644 to 755 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-deepTools-3.5.2_2 depends on package: py311-numpy>=1.16,1<1.27,1 - not found ===> Installing existing package /packages/All/py311-numpy-1.26.4_12,1.pkg [pkg.DaveG.ca] Installing py311-numpy-1.26.4_12,1... [pkg.DaveG.ca] `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] `-- Extracting gcc14-14.2.0_4: .......... done 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 ===== 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-deepTools-3.5.2_2 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> Returning to build of py311-deepTools-3.5.2_2 ===> py311-deepTools-3.5.2_2 depends on package: py311-scipy>=0.17.0 - not found ===> Installing existing package /packages/All/py311-scipy-1.11.1_5,1.pkg [pkg.DaveG.ca] Installing py311-scipy-1.11.1_5,1... [pkg.DaveG.ca] `-- Installing blas-3.12.1... [pkg.DaveG.ca] `-- Extracting blas-3.12.1: ..... done [pkg.DaveG.ca] Extracting py311-scipy-1.11.1_5,1: .......... done ===> py311-deepTools-3.5.2_2 depends on package: py311-scipy>=0.17.0 - found ===> Returning to build of py311-deepTools-3.5.2_2 ===> py311-deepTools-3.5.2_2 depends on package: py311-matplotlib>=3.3.0 - not found ===> Installing existing package /packages/All/py311-matplotlib-3.10.8.pkg [pkg.DaveG.ca] Installing py311-matplotlib-3.10.8... [pkg.DaveG.ca] `-- Installing fontconfig-2.17.1,1... [pkg.DaveG.ca] | `-- Installing expat-2.7.4... [pkg.DaveG.ca] | `-- Extracting expat-2.7.4: .......... done [pkg.DaveG.ca] | `-- Installing freetype2-2.14.1... [pkg.DaveG.ca] | | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | | `-- Installing png-1.6.55... [pkg.DaveG.ca] | | `-- Extracting png-1.6.55: .......... done [pkg.DaveG.ca] | `-- Extracting freetype2-2.14.1: .......... done [pkg.DaveG.ca] `-- Extracting fontconfig-2.17.1,1: .......... done [pkg.DaveG.ca] `-- Installing py311-contourpy-1.3.3... [pkg.DaveG.ca] `-- Extracting py311-contourpy-1.3.3: .......... done [pkg.DaveG.ca] `-- Installing py311-cycler-0.12.1... [pkg.DaveG.ca] `-- Extracting py311-cycler-0.12.1: ......... done [pkg.DaveG.ca] `-- Installing py311-fonttools-4.61.1_1... [pkg.DaveG.ca] | `-- Installing py311-brotli-1.2.0... [pkg.DaveG.ca] | `-- Extracting py311-brotli-1.2.0: ......... done [pkg.DaveG.ca] | `-- Installing py311-lxml-6.0.2... [pkg.DaveG.ca] | | `-- Installing libxml2-2.15.2... [pkg.DaveG.ca] | | `-- Extracting libxml2-2.15.2: .......... done [pkg.DaveG.ca] | | `-- Installing libxslt-1.1.45... [pkg.DaveG.ca] | | `-- Installing libgcrypt-1.12.0_1... [pkg.DaveG.ca] | | | `-- Installing libgpg-error-1.59... 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[pkg.DaveG.ca] | | | `-- Extracting libXext-1.3.6,1: .......... done [pkg.DaveG.ca] | | `-- Extracting libXScrnSaver-1.2.4_1: .......... done [pkg.DaveG.ca] | | `-- Installing libXft-2.3.8... [pkg.DaveG.ca] | | | `-- Installing libXrender-0.9.12... [pkg.DaveG.ca] | | | `-- Extracting libXrender-0.9.12: ....... done [pkg.DaveG.ca] | | `-- Extracting libXft-2.3.8: .......... done [pkg.DaveG.ca] | | `-- Extracting tk86-8.6.17: .......... done [pkg.DaveG.ca] | `-- Extracting py311-tkinter-3.11.15_11: ...... done [pkg.DaveG.ca] | `-- Installing webp-1.6.0... [pkg.DaveG.ca] | | `-- Installing giflib-5.2.2... [pkg.DaveG.ca] | | `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] | `-- Extracting webp-1.6.0: .......... done [pkg.DaveG.ca] `-- Extracting py311-pillow-11.3.0_2: .......... done [pkg.DaveG.ca] `-- Installing py311-pyparsing-3.3.2... [pkg.DaveG.ca] `-- Extracting py311-pyparsing-3.3.2: .......... done [pkg.DaveG.ca] `-- Installing py311-python-dateutil-2.9.0... [pkg.DaveG.ca] | `-- Installing py311-six-1.17.0... [pkg.DaveG.ca] | `-- Extracting py311-six-1.17.0: ........ done [pkg.DaveG.ca] `-- Extracting py311-python-dateutil-2.9.0: .......... done [pkg.DaveG.ca] `-- Installing qhull-8.0.2_3,1... [pkg.DaveG.ca] `-- Extracting qhull-8.0.2_3,1: .......... done [pkg.DaveG.ca] Extracting py311-matplotlib-3.10.8: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gdk-pixbuf-query-loaders.ucl Generating gdk-pixbuf modules cache ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ==> Running trigger: shared-mime-info.ucl Building the Shared MIME-Info database cache ===== Message from freetype2-2.14.1: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from libraqm-0.10.3: -- ===> NOTICE: The libraqm port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> py311-deepTools-3.5.2_2 depends on package: py311-matplotlib>=3.3.0 - found ===> Returning to build of py311-deepTools-3.5.2_2 ===> py311-deepTools-3.5.2_2 depends on package: py311-pysam>=0.14.0 - 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 libidn2-2.3.8... 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[pkg.DaveG.ca] `-- Extracting py311-cython-3.2.4: .......... 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-deepTools-3.5.2_2 depends on package: py311-pysam>=0.14.0 - found ===> Returning to build of py311-deepTools-3.5.2_2 ===> py311-deepTools-3.5.2_2 depends on package: py311-py2bit>=0.3.0 - not found ===> Installing existing package /packages/All/py311-py2bit-0.3.0_1.pkg [pkg.DaveG.ca] Installing py311-py2bit-0.3.0_1... [pkg.DaveG.ca] Extracting py311-py2bit-0.3.0_1: .......... done ===> py311-deepTools-3.5.2_2 depends on package: py311-py2bit>=0.3.0 - found ===> Returning to build of py311-deepTools-3.5.2_2 ===> py311-deepTools-3.5.2_2 depends on package: py311-numpydoc>=0.5 - not found ===> Installing existing package /packages/All/py311-numpydoc-1.6.0_1.pkg [pkg.DaveG.ca] Installing py311-numpydoc-1.6.0_1... [pkg.DaveG.ca] `-- Installing py311-Jinja2-3.1.6... [pkg.DaveG.ca] | `-- Installing py311-Babel-2.18.0... [pkg.DaveG.ca] | `-- Extracting py311-Babel-2.18.0: .......... done [pkg.DaveG.ca] | `-- Installing py311-markupsafe-3.0.3... [pkg.DaveG.ca] | `-- Extracting py311-markupsafe-3.0.3: .......... done [pkg.DaveG.ca] `-- Extracting py311-Jinja2-3.1.6: .......... done [pkg.DaveG.ca] `-- Installing py311-sphinx-5.3.0_3,1... [pkg.DaveG.ca] | `-- Installing ca_root_nss-3.117_2... [pkg.DaveG.ca] | `-- Extracting ca_root_nss-3.117_2: .. done [pkg.DaveG.ca] | `-- Installing py311-alabaster-0.7.16... 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[pkg.DaveG.ca] `-- Extracting py311-tabulate-0.9.0: .......... done [pkg.DaveG.ca] Extracting py311-numpydoc-1.6.0_1: .......... done ===== Message from ca_root_nss-3.117_2: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificate discovery for software that either uses other cryptographic libraries than OpenSSL, or use OpenSSL but do not follow recommended practice. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem ===== Message from py311-urllib3-2.6.3,1: -- Since version 1.25 HTTPS connections are now verified by default which is done via "cert_reqs = 'CERT_REQUIRED'". While certificate verification can be disabled via "cert_reqs = 'CERT_NONE'", it's highly recommended to leave it on. Various consumers of net/py-urllib3 already have implemented routines that either explicitly enable or disable HTTPS certificate verification (e.g. via configuration settings, CLI arguments, etc.). Yet it may happen that there are still some consumers which don't explicitly enable/disable certificate verification for HTTPS connections which could then lead to errors (as is often the case with self-signed certificates). In case of an error one should try first to temporarily disable certificate verification of the problematic urllib3 consumer to see if that approach will remedy the issue. ===> py311-deepTools-3.5.2_2 depends on package: py311-numpydoc>=0.5 - found ===> Returning to build of py311-deepTools-3.5.2_2 ===> py311-deepTools-3.5.2_2 depends on package: py311-pyBigWig>=0.3.18 - 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-deepTools-3.5.2_2 depends on package: py311-pyBigWig>=0.3.18 - found ===> Returning to build of py311-deepTools-3.5.2_2 ===> py311-deepTools-3.5.2_2 depends on package: py311-plotly>=4.9 - not found ===> Installing existing package /packages/All/py311-plotly-5.24.1_1.pkg [pkg.DaveG.ca] Installing py311-plotly-5.24.1_1... [pkg.DaveG.ca] `-- Installing py311-tenacity-9.0.0... [pkg.DaveG.ca] `-- Extracting py311-tenacity-9.0.0: .......... done [pkg.DaveG.ca] Extracting py311-plotly-5.24.1_1: .......... done ===> py311-deepTools-3.5.2_2 depends on package: py311-plotly>=4.9 - found ===> Returning to build of py311-deepTools-3.5.2_2 ===> py311-deepTools-3.5.2_2 depends on package: py311-deeptoolsintervals>=0.1.8 - not found ===> Installing existing package /packages/All/py311-deeptoolsintervals-0.1.9_1.pkg [pkg.DaveG.ca] Installing py311-deeptoolsintervals-0.1.9_1... [pkg.DaveG.ca] Extracting py311-deeptoolsintervals-0.1.9_1: .......... done ===> py311-deepTools-3.5.2_2 depends on package: py311-deeptoolsintervals>=0.1.8 - found ===> Returning to build of py311-deepTools-3.5.2_2 ===> py311-deepTools-3.5.2_2 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py311-deepTools-3.5.2_2 ===> 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 deepTools.egg-info/PKG-INFO writing dependency_links to deepTools.egg-info/dependency_links.txt writing requirements to deepTools.egg-info/requires.txt writing top-level names to deepTools.egg-info/top_level.txt reading manifest file 'deepTools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'examples/*' warning: no previously-included files found matching 'deeptools/test/*' warning: no previously-included files found matching 'galaxy/*' warning: no previously-included files found matching 'gallery/*' adding license file 'LICENSE.txt' writing manifest file 'deepTools.egg-info/SOURCES.txt' running build_scripts running install_lib creating /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11 creating /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/sumCoveragePerBin.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/countReadsPerBin.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/plotEnrichment.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/estimateReadFiltering.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/computeMatrixOperations.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/getScaleFactor.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/alignmentSieve.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/bigwigCompare.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/getScorePerBigWigBin.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/correlation.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/parserCommon.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/plotPCA.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/__init__.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/deepBlue.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/correctGCBias.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/bamPEFragmentSize.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/correlation_heatmap.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/writeBedGraph_bam_and_bw.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/heatmapper_utilities.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/multiBamSummary.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/multiBigwigSummary.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/plotHeatmap.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/bamHandler.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/bigwigAverage.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/SES_scaleFactor.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/misc.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/getRatio.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/mapReduce.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/writeBedGraph.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/utilities.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/plotFingerprint.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/cm.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/plotCoverage.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/getFragmentAndReadSize.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/deeptools_list_tools.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/bamCompare.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/plotCorrelation.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/computeMatrix.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/plotProfile.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/computeGCBias.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/heatmapper.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/bamCoverage.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools copying build/lib/deeptools/_version.py -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/sumCoveragePerBin.py to sumCoveragePerBin.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/countReadsPerBin.py to countReadsPerBin.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/plotEnrichment.py to plotEnrichment.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/estimateReadFiltering.py to estimateReadFiltering.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/computeMatrixOperations.py to computeMatrixOperations.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/getScaleFactor.py to getScaleFactor.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/alignmentSieve.py to alignmentSieve.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/bigwigCompare.py to bigwigCompare.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/getScorePerBigWigBin.py to getScorePerBigWigBin.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/correlation.py to correlation.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/parserCommon.py to parserCommon.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/plotPCA.py to plotPCA.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/deepBlue.py to deepBlue.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/correctGCBias.py to correctGCBias.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/bamPEFragmentSize.py to bamPEFragmentSize.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/correlation_heatmap.py to correlation_heatmap.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/writeBedGraph_bam_and_bw.py to writeBedGraph_bam_and_bw.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/heatmapper_utilities.py to heatmapper_utilities.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/multiBamSummary.py to multiBamSummary.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/multiBigwigSummary.py to multiBigwigSummary.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/plotHeatmap.py to plotHeatmap.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/bamHandler.py to bamHandler.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/bigwigAverage.py to bigwigAverage.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/SES_scaleFactor.py to SES_scaleFactor.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/misc.py to misc.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/getRatio.py to getRatio.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/mapReduce.py to mapReduce.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/writeBedGraph.py to writeBedGraph.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/utilities.py to utilities.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/plotFingerprint.py to plotFingerprint.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/cm.py to cm.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/plotCoverage.py to plotCoverage.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/getFragmentAndReadSize.py to getFragmentAndReadSize.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/deeptools_list_tools.py to deeptools_list_tools.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/bamCompare.py to bamCompare.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/plotCorrelation.py to plotCorrelation.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/computeMatrix.py to computeMatrix.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/plotProfile.py to plotProfile.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/computeGCBias.py to computeGCBias.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/heatmapper.py to heatmapper.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/bamCoverage.py to bamCoverage.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deeptools/_version.py to _version.cpython-311.pyc writing byte-compilation script '/tmp/tmpa2vq1_fg.py' /usr/local/bin/python3.11 /tmp/tmpa2vq1_fg.py removing /tmp/tmpa2vq1_fg.py running install_egg_info Copying deepTools.egg-info to /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/lib/python3.11/site-packages/deepTools-3.5.2-py3.11.egg-info running install_scripts copying build/scripts-3.11/plotEnrichment -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/bigwigCompare -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/alignmentSieve -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/bamPEFragmentSize -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/computeMatrix -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/multiBigwigSummary -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/estimateReadFiltering -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/multiBamSummary -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/plotHeatmap -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/plotCorrelation -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/plotPCA -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/estimateScaleFactor -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/plotCoverage -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/plotProfile -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/bigwigAverage -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/correctGCBias -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/deeptools -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/computeMatrixOperations -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/computeGCBias -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/bamCompare -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/bamCoverage -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin copying build/scripts-3.11/plotFingerprint -> /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/plotEnrichment to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/bigwigCompare to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/alignmentSieve to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/bamPEFragmentSize to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/computeMatrix to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/multiBigwigSummary to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/estimateReadFiltering to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/multiBamSummary to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/plotHeatmap to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/plotCorrelation to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/plotPCA to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/estimateScaleFactor to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/plotCoverage to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/plotProfile to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/bigwigAverage to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/correctGCBias to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/deeptools to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/computeMatrixOperations to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/computeGCBias to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/bamCompare to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/bamCoverage to 755 changing mode of /wrkdirs/usr/ports/biology/py-deeptools/work-py311/stage/usr/local/bin/plotFingerprint to 755 writing list of installed files to '/wrkdirs/usr/ports/biology/py-deeptools/work-py311/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/plotEnrichment --> bin/plotEnrichment-3.11 Link: @bin/plotEnrichment --> bin/plotEnrichment-3.11 Move: bin/bigwigCompare --> bin/bigwigCompare-3.11 Link: @bin/bigwigCompare --> bin/bigwigCompare-3.11 Move: bin/alignmentSieve --> bin/alignmentSieve-3.11 Link: @bin/alignmentSieve --> bin/alignmentSieve-3.11 Move: bin/bamPEFragmentSize --> bin/bamPEFragmentSize-3.11 Link: @bin/bamPEFragmentSize --> bin/bamPEFragmentSize-3.11 Move: bin/computeMatrix --> bin/computeMatrix-3.11 Link: @bin/computeMatrix --> bin/computeMatrix-3.11 Move: bin/multiBigwigSummary --> bin/multiBigwigSummary-3.11 Link: @bin/multiBigwigSummary --> bin/multiBigwigSummary-3.11 Move: bin/estimateReadFiltering --> bin/estimateReadFiltering-3.11 Link: @bin/estimateReadFiltering --> bin/estimateReadFiltering-3.11 Move: bin/multiBamSummary --> bin/multiBamSummary-3.11 Link: @bin/multiBamSummary --> bin/multiBamSummary-3.11 Move: bin/plotHeatmap --> bin/plotHeatmap-3.11 Link: @bin/plotHeatmap --> bin/plotHeatmap-3.11 Move: bin/plotCorrelation --> bin/plotCorrelation-3.11 Link: @bin/plotCorrelation --> bin/plotCorrelation-3.11 Move: bin/plotPCA --> bin/plotPCA-3.11 Link: @bin/plotPCA --> bin/plotPCA-3.11 Move: bin/estimateScaleFactor --> bin/estimateScaleFactor-3.11 Link: @bin/estimateScaleFactor --> bin/estimateScaleFactor-3.11 Move: bin/plotCoverage --> bin/plotCoverage-3.11 Link: @bin/plotCoverage --> bin/plotCoverage-3.11 Move: bin/plotProfile --> bin/plotProfile-3.11 Link: @bin/plotProfile --> bin/plotProfile-3.11 Move: bin/bigwigAverage --> bin/bigwigAverage-3.11 Link: @bin/bigwigAverage --> bin/bigwigAverage-3.11 Move: bin/correctGCBias --> bin/correctGCBias-3.11 Link: @bin/correctGCBias --> bin/correctGCBias-3.11 Move: bin/deeptools --> bin/deeptools-3.11 Link: @bin/deeptools --> bin/deeptools-3.11 Move: bin/computeMatrixOperations --> bin/computeMatrixOperations-3.11 Link: @bin/computeMatrixOperations --> bin/computeMatrixOperations-3.11 Move: bin/computeGCBias --> bin/computeGCBias-3.11 Link: @bin/computeGCBias --> bin/computeGCBias-3.11 Move: bin/bamCompare --> bin/bamCompare-3.11 Link: @bin/bamCompare --> bin/bamCompare-3.11 Move: bin/bamCoverage --> bin/bamCoverage-3.11 Link: @bin/bamCoverage --> bin/bamCoverage-3.11 Move: bin/plotFingerprint --> bin/plotFingerprint-3.11 Link: @bin/plotFingerprint --> bin/plotFingerprint-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=2026-03-19T00:23:47+0000' 'PKG_NOTE_ports_top_git_hash=8c988f802ea2' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=b304d8ab18ac' '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-deepTools-3.5.2_2 ===> Building py311-deepTools-3.5.2_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-deepTools-3.5.2_2 build of biology/py-deeptools@py311 | py311-deepTools-3.5.2_2 ended at Wed Mar 18 20:27:39 EDT 2026 build time: 00:03:59