=>> Building biology/checkm build started at Sun May 4 00:57:34 BST 2025 port directory: /usr/ports/biology/checkm package name: CheckM-1.2.3_1 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 802 Apr 5 02:48 /usr/ports/biology/checkm/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 3b5eced32d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 04 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE 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/14-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/14-amd64-default-dan/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/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= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/checkm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/checkm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/checkm/work/.cache HOME=/wrkdirs/usr/ports/biology/checkm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/checkm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/checkm/work/.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/checkm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/checkm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/checkm/work/.cache HOME=/wrkdirs/usr/ports/biology/checkm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/checkm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/checkm/work/.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 " 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=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/CheckM" EXAMPLESDIR="share/examples/CheckM" DATADIR="share/CheckM" WWWDIR="www/CheckM" ETCDIR="etc/CheckM" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/CheckM DOCSDIR=/usr/local/share/doc/CheckM EXAMPLESDIR=/usr/local/share/examples/CheckM WWWDIR=/usr/local/www/CheckM ETCDIR=/usr/local/etc/CheckM --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 apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.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 pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Depends on expired science/py-DendroPy. It is scheduled to be removed on or after 2025-06-01. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> CheckM-1.2.3_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> CheckM-1.2.3_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of CheckM-1.2.3_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Depends on expired science/py-DendroPy. It is scheduled to be removed on or after 2025-06-01. ===> Fetching all distfiles required by CheckM-1.2.3_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Depends on expired science/py-DendroPy. It is scheduled to be removed on or after 2025-06-01. ===> Fetching all distfiles required by CheckM-1.2.3_1 for building => SHA256 Checksum OK for Ecogenomics-CheckM-v1.2.3_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Depends on expired science/py-DendroPy. It is scheduled to be removed on or after 2025-06-01. ===> Fetching all distfiles required by CheckM-1.2.3_1 for building ===> Extracting for CheckM-1.2.3_1 => SHA256 Checksum OK for Ecogenomics-CheckM-v1.2.3_GH0.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 CheckM-1.2.3_1 ===> Converting DOS text files to UNIX text files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> CheckM-1.2.3_1 depends on package: py311-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py311-setuptools-63.1.0_3.pkg [pkg-builder.dan.net.uk] Installing py311-setuptools-63.1.0_3... [pkg-builder.dan.net.uk] `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] Extracting py311-setuptools-63.1.0_3: .......... done ===== Message from python311-3.11.12: -- 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 ===> CheckM-1.2.3_1 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of CheckM-1.2.3_1 ===> CheckM-1.2.3_1 depends on file: /usr/local/bin/python3.11 - found ===> CheckM-1.2.3_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] 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. ===> CheckM-1.2.3_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of CheckM-1.2.3_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 CheckM-1.2.3_1 running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for CheckM-1.2.3_1 running build running build_py creating build creating build/lib creating build/lib/checkm copying checkm/customHelpFormatter.py -> build/lib/checkm copying checkm/hmmerAligner.py -> build/lib/checkm copying checkm/main.py -> build/lib/checkm copying checkm/timeKeeper.py -> build/lib/checkm copying checkm/aminoAcidIdentity.py -> build/lib/checkm copying checkm/common.py -> build/lib/checkm copying checkm/__init__.py -> build/lib/checkm copying checkm/profile.py -> build/lib/checkm copying checkm/resultsParser.py -> build/lib/checkm copying checkm/binStatistics.py -> build/lib/checkm copying checkm/merger.py -> build/lib/checkm copying checkm/binTools.py -> build/lib/checkm copying checkm/hmmer.py -> build/lib/checkm copying checkm/checkmData.py -> build/lib/checkm copying checkm/treeParser.py -> build/lib/checkm copying checkm/unbinned.py -> build/lib/checkm copying checkm/defaultValues.py -> build/lib/checkm copying checkm/fileEntity.py -> build/lib/checkm copying checkm/logger.py -> build/lib/checkm copying checkm/genomicSignatures.py -> build/lib/checkm copying checkm/coverageWindows.py -> build/lib/checkm copying checkm/coverage.py -> build/lib/checkm copying checkm/markerGeneFinder.py -> build/lib/checkm copying checkm/hmmerModelParser.py -> build/lib/checkm copying checkm/uniqueMarkers.py -> build/lib/checkm copying checkm/prodigal.py -> build/lib/checkm copying checkm/taxonParser.py -> build/lib/checkm copying checkm/pplacer.py -> build/lib/checkm copying checkm/markerSets.py -> build/lib/checkm copying checkm/manifestManager.py -> build/lib/checkm copying checkm/ssuFinder.py -> build/lib/checkm copying checkm/prettytable.py -> build/lib/checkm creating build/lib/checkm/plot copying checkm/plot/AbstractPlot.py -> build/lib/checkm/plot copying checkm/plot/gcPlots.py -> build/lib/checkm/plot copying checkm/plot/nxPlot.py -> build/lib/checkm/plot copying checkm/plot/__init__.py -> build/lib/checkm/plot copying checkm/plot/gcBiasPlots.py -> build/lib/checkm/plot copying checkm/plot/distributionPlots.py -> build/lib/checkm/plot copying checkm/plot/lengthHistogram.py -> build/lib/checkm/plot copying checkm/plot/tetraDistPlots.py -> build/lib/checkm/plot copying checkm/plot/codingDensityPlots.py -> build/lib/checkm/plot copying checkm/plot/markerGenePosPlot.py -> build/lib/checkm/plot creating build/lib/checkm/test copying checkm/test/test_markerSets.py -> build/lib/checkm/test copying checkm/test/test_taxonomyUtils.py -> build/lib/checkm/test copying checkm/test/test_ecoli.py -> build/lib/checkm/test copying checkm/test/test_binStatistics.py -> build/lib/checkm/test copying checkm/test/__init__.py -> build/lib/checkm/test copying checkm/test/test_aminoAcidIdentity.py -> build/lib/checkm/test copying checkm/test/test_seqUtils.py -> build/lib/checkm/test copying checkm/test/test_genomicSignatures.py -> build/lib/checkm/test creating build/lib/checkm/util copying checkm/util/taxonomyUtils.py -> build/lib/checkm/util copying checkm/util/__init__.py -> build/lib/checkm/util copying checkm/util/img.py -> build/lib/checkm/util copying checkm/util/seqUtils.py -> build/lib/checkm/util copying checkm/util/pfam.py -> build/lib/checkm/util running egg_info creating checkm_genome.egg-info writing checkm_genome.egg-info/PKG-INFO writing dependency_links to checkm_genome.egg-info/dependency_links.txt writing requirements to checkm_genome.egg-info/requires.txt writing top-level names to checkm_genome.egg-info/top_level.txt writing manifest file 'checkm_genome.egg-info/SOURCES.txt' reading manifest file 'checkm_genome.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.txt' under directory 'docs' adding license file 'LICENSE' writing manifest file 'checkm_genome.egg-info/SOURCES.txt' copying checkm/DATA_CONFIG -> build/lib/checkm copying checkm/VERSION -> build/lib/checkm running build_scripts creating build/scripts-3.11 copying and adjusting bin/checkm -> build/scripts-3.11 changing mode of build/scripts-3.11/checkm from 644 to 755 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> CheckM-1.2.3_1 depends on package: py311-numpy>=1.16,1<1.27,1 - not found ===> Installing existing package /packages/All/py311-numpy-1.26.4_6,1.pkg [pkg-builder.dan.net.uk] Installing py311-numpy-1.26.4_6,1... [pkg-builder.dan.net.uk] `-- Installing gcc13-13.3.0_2... [pkg-builder.dan.net.uk] | `-- Installing binutils-2.44,1... [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] | `-- Extracting binutils-2.44,1: .......... 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-4.2.2,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] `-- Extracting gcc13-13.3.0_2: .......... 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-0.3.29_1,2... [pkg-builder.dan.net.uk] `-- Extracting openblas-0.3.29_1,2: .......... done [pkg-builder.dan.net.uk] `-- Installing suitesparse-umfpack-6.3.5_1... [pkg-builder.dan.net.uk] | `-- Installing suitesparse-amd-3.3.3... [pkg-builder.dan.net.uk] | | `-- Installing suitesparse-config-7.10.2... [pkg-builder.dan.net.uk] | | `-- Extracting suitesparse-config-7.10.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-amd-3.3.3: .......... done [pkg-builder.dan.net.uk] | `-- Installing suitesparse-camd-3.3.3... [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-camd-3.3.3: .......... done [pkg-builder.dan.net.uk] | `-- Installing suitesparse-ccolamd-3.3.4... [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-ccolamd-3.3.4: .......... done [pkg-builder.dan.net.uk] | `-- Installing suitesparse-cholmod-5.3.2... [pkg-builder.dan.net.uk] | | `-- Installing suitesparse-colamd-3.3.4... [pkg-builder.dan.net.uk] | | `-- Extracting suitesparse-colamd-3.3.4: .......... done [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-cholmod-5.3.2: .......... done [pkg-builder.dan.net.uk] `-- Extracting suitesparse-umfpack-6.3.5_1: .......... done [pkg-builder.dan.net.uk] Extracting py311-numpy-1.26.4_6,1: .......... done ===== Message from gcc13-13.3.0_2: -- 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. ===> CheckM-1.2.3_1 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> Returning to build of CheckM-1.2.3_1 ===> CheckM-1.2.3_1 depends on package: py311-DendroPy>0 - not found ===> Installing existing package /packages/All/py311-DendroPy-5.0.1_1.pkg [pkg-builder.dan.net.uk] Installing py311-DendroPy-5.0.1_1... [pkg-builder.dan.net.uk] Extracting py311-DendroPy-5.0.1_1: .......... done ===== Message from py311-DendroPy-5.0.1_1: -- If you use this library either in whole or in part in your analysis, or use any code derived from it, please cite it as: Sukumaran, J. and Mark T. Holder. 2010. DendroPy: A Python library for phylogenetic computing. Bioinformatics 26: 1569-1571. -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Depends on expired devel/py-pytest-runner. It is scheduled to be removed on or after 2025-03-31. ===> CheckM-1.2.3_1 depends on package: py311-DendroPy>0 - found ===> Returning to build of CheckM-1.2.3_1 ===> CheckM-1.2.3_1 depends on package: py311-matplotlib>0 - not found ===> Installing existing package /packages/All/py311-matplotlib-3.8.0_1.pkg [pkg-builder.dan.net.uk] Installing py311-matplotlib-3.8.0_1... [pkg-builder.dan.net.uk] `-- Installing fontconfig-2.15.0_3,1... [pkg-builder.dan.net.uk] | `-- Installing expat-2.7.1... [pkg-builder.dan.net.uk] | `-- Extracting expat-2.7.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing freetype2-2.13.3... [pkg-builder.dan.net.uk] | `-- Extracting freetype2-2.13.3: .......... done [pkg-builder.dan.net.uk] `-- Extracting fontconfig-2.15.0_3,1: .......... done [pkg-builder.dan.net.uk] `-- Installing png-1.6.47... [pkg-builder.dan.net.uk] `-- Extracting png-1.6.47: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-certifi-2025.1.31... [pkg-builder.dan.net.uk] `-- Extracting py311-certifi-2025.1.31: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-contourpy-1.3.2... [pkg-builder.dan.net.uk] `-- Extracting py311-contourpy-1.3.2: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-cycler-0.12.1... [pkg-builder.dan.net.uk] `-- Extracting py311-cycler-0.12.1: ......... done [pkg-builder.dan.net.uk] `-- Installing py311-fonttools-4.57.0... [pkg-builder.dan.net.uk] | `-- Installing py311-fs2-2.4.16_1... [pkg-builder.dan.net.uk] | | `-- Installing py311-appdirs-1.4.4_1... [pkg-builder.dan.net.uk] | | `-- Extracting py311-appdirs-1.4.4_1: ........ done [pkg-builder.dan.net.uk] | | `-- Installing py311-pytz-2024.2_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting py311-pytz-2024.2_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing py311-six-1.17.0... [pkg-builder.dan.net.uk] | | `-- Extracting py311-six-1.17.0: ........ done [pkg-builder.dan.net.uk] | `-- Extracting py311-fs2-2.4.16_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-lxml-4.9.3_1... [pkg-builder.dan.net.uk] | | `-- Installing libxml2-2.11.9... [pkg-builder.dan.net.uk] | | `-- Extracting libxml2-2.11.9: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libxslt-1.1.42... [pkg-builder.dan.net.uk] | | `-- Installing libgcrypt-1.11.0... [pkg-builder.dan.net.uk] | | | `-- Installing libgpg-error-1.55... [pkg-builder.dan.net.uk] | | | `-- Extracting libgpg-error-1.55: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libgcrypt-1.11.0: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libxslt-1.1.42: .......... done [pkg-builder.dan.net.uk] | `-- Extracting py311-lxml-4.9.3_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-unicodedata2-16.0.0... [pkg-builder.dan.net.uk] | `-- Extracting py311-unicodedata2-16.0.0: ...... done [pkg-builder.dan.net.uk] `-- Extracting py311-fonttools-4.57.0: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-importlib-resources-6.5.2... [pkg-builder.dan.net.uk] `-- Extracting py311-importlib-resources-6.5.2: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-kiwisolver-1.4.8,1... [pkg-builder.dan.net.uk] `-- Extracting py311-kiwisolver-1.4.8,1: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-packaging-24.2... [pkg-builder.dan.net.uk] `-- Extracting py311-packaging-24.2: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-pillow-11.0.0... [pkg-builder.dan.net.uk] | `-- Installing jpeg-turbo-3.1.0... [pkg-builder.dan.net.uk] | `-- Extracting jpeg-turbo-3.1.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing lcms2-2.17... [pkg-builder.dan.net.uk] | | `-- Installing tiff-4.7.0... [pkg-builder.dan.net.uk] | | `-- Installing jbigkit-2.1_3... [pkg-builder.dan.net.uk] | | `-- Extracting jbigkit-2.1_3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing lerc-4.0.0... [pkg-builder.dan.net.uk] | | `-- Extracting lerc-4.0.0: ..... done [pkg-builder.dan.net.uk] | | `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] | | `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting tiff-4.7.0: .......... done [pkg-builder.dan.net.uk] | `-- Extracting lcms2-2.17: .......... done [pkg-builder.dan.net.uk] | `-- Installing libimagequant-4.3.4_2... [pkg-builder.dan.net.uk] | `-- Extracting libimagequant-4.3.4_2: ...... done [pkg-builder.dan.net.uk] | `-- Installing libraqm-0.10.2... [pkg-builder.dan.net.uk] | | `-- Installing fribidi-1.0.16... [pkg-builder.dan.net.uk] | | `-- Extracting fribidi-1.0.16: .......... done [pkg-builder.dan.net.uk] | | `-- Installing harfbuzz-10.3.0... [pkg-builder.dan.net.uk] | | `-- Installing glib-2.84.1_2,2... [pkg-builder.dan.net.uk] | | | `-- Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] | | | `-- Extracting libiconv-1.17_1: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing libinotify-20240724_1... [pkg-builder.dan.net.uk] | | | `-- Extracting libinotify-20240724_1: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing pcre2-10.45_1... [pkg-builder.dan.net.uk] | | | `-- Extracting pcre2-10.45_1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting glib-2.84.1_2,2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing graphite2-1.3.14... [pkg-builder.dan.net.uk] | | `-- Extracting graphite2-1.3.14: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting harfbuzz-10.3.0: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libraqm-0.10.2: .......... done [pkg-builder.dan.net.uk] | `-- Installing libxcb-1.17.0... [pkg-builder.dan.net.uk] | | `-- Installing libXau-1.0.11... [pkg-builder.dan.net.uk] | | `-- Extracting libXau-1.0.11: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXdmcp-1.1.5... [pkg-builder.dan.net.uk] | | `-- Installing xorgproto-2024.1... [pkg-builder.dan.net.uk] | | `-- Extracting xorgproto-2024.1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg-builder.dan.net.uk] | `-- Extracting libxcb-1.17.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing openjpeg-2.5.3... [pkg-builder.dan.net.uk] | `-- Extracting openjpeg-2.5.3: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-olefile-0.46_1... [pkg-builder.dan.net.uk] | `-- Extracting py311-olefile-0.46_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-tkinter-3.11.12_10... [pkg-builder.dan.net.uk] | | `-- Installing tcl86-8.6.16_2... [pkg-builder.dan.net.uk] | | `-- Extracting tcl86-8.6.16_2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing tk86-8.6.16... [pkg-builder.dan.net.uk] | | `-- Installing libX11-1.8.12,1... [pkg-builder.dan.net.uk] | | `-- Extracting libX11-1.8.12,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXScrnSaver-1.2.4_1... [pkg-builder.dan.net.uk] | | | `-- Installing libXext-1.3.6,1... [pkg-builder.dan.net.uk] | | | `-- Extracting libXext-1.3.6,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libXScrnSaver-1.2.4_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXft-2.3.8... [pkg-builder.dan.net.uk] | | | `-- Installing libXrender-0.9.12... [pkg-builder.dan.net.uk] | | | `-- Extracting libXrender-0.9.12: ....... done [pkg-builder.dan.net.uk] | | `-- Extracting libXft-2.3.8: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting tk86-8.6.16: .......... done [pkg-builder.dan.net.uk] | `-- Extracting py311-tkinter-3.11.12_10: ...... done [pkg-builder.dan.net.uk] | `-- Installing webp-1.5.0... [pkg-builder.dan.net.uk] | | `-- Installing freeglut-3.2.1... [pkg-builder.dan.net.uk] | | `-- Installing libGLU-9.0.3... [pkg-builder.dan.net.uk] | | | `-- Installing libglvnd-1.7.0... [pkg-builder.dan.net.uk] | | | `-- Extracting libglvnd-1.7.0: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libGLU-9.0.3: ..... done [pkg-builder.dan.net.uk] | | `-- Installing libICE-1.1.1,1... [pkg-builder.dan.net.uk] | | `-- Extracting libICE-1.1.1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXi-1.8.1,1... [pkg-builder.dan.net.uk] | | | `-- Installing libXfixes-6.0.1... [pkg-builder.dan.net.uk] | | | `-- Extracting libXfixes-6.0.1: ....... done [pkg-builder.dan.net.uk] | | `-- Extracting libXi-1.8.1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXrandr-1.5.4... [pkg-builder.dan.net.uk] | | `-- Extracting libXrandr-1.5.4: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXxf86vm-1.1.5... [pkg-builder.dan.net.uk] | | `-- Extracting libXxf86vm-1.1.5: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting freeglut-3.2.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing giflib-5.2.2... [pkg-builder.dan.net.uk] | | `-- Extracting giflib-5.2.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting webp-1.5.0: .......... done [pkg-builder.dan.net.uk] `-- Extracting py311-pillow-11.0.0: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-pluggy-1.5.0... [pkg-builder.dan.net.uk] `-- Extracting py311-pluggy-1.5.0: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-pyparsing-3.2.3... [pkg-builder.dan.net.uk] `-- Extracting py311-pyparsing-3.2.3: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-python-dateutil-2.9.0... [pkg-builder.dan.net.uk] `-- Extracting py311-python-dateutil-2.9.0: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-tornado-6.4... [pkg-builder.dan.net.uk] `-- Extracting py311-tornado-6.4: .......... done [pkg-builder.dan.net.uk] `-- Installing qhull-8.0.2_3,1... [pkg-builder.dan.net.uk] `-- Extracting qhull-8.0.2_3,1: .......... done [pkg-builder.dan.net.uk] Extracting py311-matplotlib-3.8.0_1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from freetype2-2.13.3: -- 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 libimagequant-4.3.4_2: -- ===> NOTICE: The libimagequant 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 ===== Message from libinotify-20240724_1: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from freeglut-3.2.1: -- Joystick support is untested and it is unknown if it works. Do not hesitate to contact x11@FreeBSD.org if this causes issues. ===> CheckM-1.2.3_1 depends on package: py311-matplotlib>0 - found ===> Returning to build of CheckM-1.2.3_1 ===> CheckM-1.2.3_1 depends on package: py311-pysam>0 - not found ===> Installing existing package /packages/All/py311-pysam-0.23.0_1.pkg [pkg-builder.dan.net.uk] Installing py311-pysam-0.23.0_1... [pkg-builder.dan.net.uk] `-- Installing bcftools-1.21... [pkg-builder.dan.net.uk] | `-- Installing bash-5.2.37... [pkg-builder.dan.net.uk] | `-- Extracting bash-5.2.37: .......... done [pkg-builder.dan.net.uk] | `-- Installing gsl-2.7.1_1... [pkg-builder.dan.net.uk] | `-- Extracting gsl-2.7.1_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing htslib-1.21... [pkg-builder.dan.net.uk] | | `-- Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] | | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | | | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | | | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] | | `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] | | `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | | `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting curl-8.13.0_1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting htslib-1.21: .......... done [pkg-builder.dan.net.uk] | `-- Installing perl5-5.36.3_3... [pkg-builder.dan.net.uk] | `-- Extracting perl5-5.36.3_3: .......... done [pkg-builder.dan.net.uk] `-- Extracting bcftools-1.21: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-cython-0.29.37_2... [pkg-builder.dan.net.uk] `-- Extracting py311-cython-0.29.37_2: .......... done [pkg-builder.dan.net.uk] `-- Installing samtools-1.21... [pkg-builder.dan.net.uk] `-- Extracting samtools-1.21: .......... done [pkg-builder.dan.net.uk] Extracting py311-pysam-0.23.0_1: .......... done ===> CheckM-1.2.3_1 depends on package: py311-pysam>0 - found ===> Returning to build of CheckM-1.2.3_1 ===> CheckM-1.2.3_1 depends on package: py311-scipy>0 - not found ===> Installing existing package /packages/All/py311-scipy-1.11.1_4,1.pkg [pkg-builder.dan.net.uk] Installing py311-scipy-1.11.1_4,1... [pkg-builder.dan.net.uk] `-- Installing blas-3.12.1... [pkg-builder.dan.net.uk] `-- Extracting blas-3.12.1: ..... done [pkg-builder.dan.net.uk] Extracting py311-scipy-1.11.1_4,1: .......... done ===> CheckM-1.2.3_1 depends on package: py311-scipy>0 - found ===> Returning to build of CheckM-1.2.3_1 ===> CheckM-1.2.3_1 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for CheckM-1.2.3_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 checkm_genome.egg-info/PKG-INFO writing dependency_links to checkm_genome.egg-info/dependency_links.txt writing requirements to checkm_genome.egg-info/requires.txt writing top-level names to checkm_genome.egg-info/top_level.txt reading manifest file 'checkm_genome.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.txt' under directory 'docs' adding license file 'LICENSE' writing manifest file 'checkm_genome.egg-info/SOURCES.txt' running build_scripts running install_lib creating /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11 creating /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm creating /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot copying build/lib/checkm/plot/AbstractPlot.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot copying build/lib/checkm/plot/gcPlots.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot copying build/lib/checkm/plot/nxPlot.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot copying build/lib/checkm/plot/__init__.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot copying build/lib/checkm/plot/gcBiasPlots.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot copying build/lib/checkm/plot/distributionPlots.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot copying build/lib/checkm/plot/lengthHistogram.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot copying build/lib/checkm/plot/tetraDistPlots.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot copying build/lib/checkm/plot/codingDensityPlots.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot copying build/lib/checkm/plot/markerGenePosPlot.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot copying build/lib/checkm/customHelpFormatter.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm creating /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/util copying build/lib/checkm/util/taxonomyUtils.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/util copying build/lib/checkm/util/__init__.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/util copying build/lib/checkm/util/img.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/util copying build/lib/checkm/util/seqUtils.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/util copying build/lib/checkm/util/pfam.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/util copying build/lib/checkm/hmmerAligner.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/main.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/DATA_CONFIG -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/timeKeeper.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/aminoAcidIdentity.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/common.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/__init__.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/profile.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/resultsParser.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/binStatistics.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/VERSION -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/merger.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/binTools.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/hmmer.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/checkmData.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/treeParser.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/unbinned.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/defaultValues.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/fileEntity.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/logger.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/genomicSignatures.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/coverageWindows.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/coverage.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/markerGeneFinder.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/hmmerModelParser.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/uniqueMarkers.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/prodigal.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm creating /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test copying build/lib/checkm/test/test_markerSets.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test copying build/lib/checkm/test/test_taxonomyUtils.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test copying build/lib/checkm/test/test_ecoli.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test copying build/lib/checkm/test/test_binStatistics.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test copying build/lib/checkm/test/__init__.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test copying build/lib/checkm/test/test_aminoAcidIdentity.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test copying build/lib/checkm/test/test_seqUtils.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test copying build/lib/checkm/test/test_genomicSignatures.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test copying build/lib/checkm/taxonParser.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/pplacer.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/markerSets.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/manifestManager.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/ssuFinder.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm copying build/lib/checkm/prettytable.py -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot/AbstractPlot.py to AbstractPlot.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot/gcPlots.py to gcPlots.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot/nxPlot.py to nxPlot.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot/gcBiasPlots.py to gcBiasPlots.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot/distributionPlots.py to distributionPlots.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot/lengthHistogram.py to lengthHistogram.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot/tetraDistPlots.py to tetraDistPlots.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot/codingDensityPlots.py to codingDensityPlots.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/plot/markerGenePosPlot.py to markerGenePosPlot.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/customHelpFormatter.py to customHelpFormatter.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/util/taxonomyUtils.py to taxonomyUtils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/util/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/util/img.py to img.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/util/seqUtils.py to seqUtils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/util/pfam.py to pfam.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/hmmerAligner.py to hmmerAligner.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/main.py to main.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/timeKeeper.py to timeKeeper.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/aminoAcidIdentity.py to aminoAcidIdentity.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/common.py to common.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/profile.py to profile.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/resultsParser.py to resultsParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/binStatistics.py to binStatistics.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/merger.py to merger.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/binTools.py to binTools.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/hmmer.py to hmmer.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/checkmData.py to checkmData.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/treeParser.py to treeParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/unbinned.py to unbinned.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/defaultValues.py to defaultValues.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/fileEntity.py to fileEntity.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/logger.py to logger.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/genomicSignatures.py to genomicSignatures.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/coverageWindows.py to coverageWindows.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/coverage.py to coverage.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/markerGeneFinder.py to markerGeneFinder.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/hmmerModelParser.py to hmmerModelParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/uniqueMarkers.py to uniqueMarkers.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/prodigal.py to prodigal.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test/test_markerSets.py to test_markerSets.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test/test_taxonomyUtils.py to test_taxonomyUtils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test/test_ecoli.py to test_ecoli.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test/test_binStatistics.py to test_binStatistics.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test/test_aminoAcidIdentity.py to test_aminoAcidIdentity.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test/test_seqUtils.py to test_seqUtils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/test/test_genomicSignatures.py to test_genomicSignatures.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/taxonParser.py to taxonParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/pplacer.py to pplacer.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/markerSets.py to markerSets.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/manifestManager.py to manifestManager.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/ssuFinder.py to ssuFinder.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm/prettytable.py to prettytable.cpython-311.pyc writing byte-compilation script '/tmp/tmpqgi44ba8.py' /usr/local/bin/python3.11 /tmp/tmpqgi44ba8.py removing /tmp/tmpqgi44ba8.py running install_egg_info Copying checkm_genome.egg-info to /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/lib/python3.11/site-packages/checkm_genome-1.2.3-py3.11.egg-info running install_scripts copying build/scripts-3.11/checkm -> /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/bin changing mode of /wrkdirs/usr/ports/biology/checkm/work/stage/usr/local/bin/checkm to 755 writing list of installed files to '/wrkdirs/usr/ports/biology/checkm/work/.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=2025-05-03T23:57:34+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=3b5eced32d' '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 CheckM-1.2.3_1 ===> Building CheckM-1.2.3_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for CheckM-1.2.3_1 build of biology/checkm | CheckM-1.2.3_1 ended at Sun May 4 00:59:42 BST 2025 build time: 00:02:08