=> Building biology/checkm Started : Wednesday, 24 JUL 2019 at 16:48:16 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.6-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.6-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/construction/biology/checkm XDG_CONFIG_HOME=/construction/biology/checkm HOME=/construction/biology/checkm TMPDIR="/tmp" PATH=/construction/biology/checkm/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/checkm XDG_CONFIG_HOME=/construction/biology/checkm HOME=/construction/biology/checkm TMPDIR="/tmp" PATH=/construction/biology/checkm/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/checkm/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=5.6 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/CheckM" EXAMPLESDIR="share/examples/CheckM" DATADIR="share/CheckM" WWWDIR="www/CheckM" ETCDIR="etc/CheckM" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.6 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500601 OSVERSION=9999999 OSREL=5.6 _OSRELEASE=5.6-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> CheckM-1.0.13_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> CheckM-1.0.13_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of CheckM-1.0.13_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by CheckM-1.0.13_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by CheckM-1.0.13_1 for building => SHA256 Checksum OK for Ecogenomics-CheckM-v1.0.13_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by CheckM-1.0.13_1 for building ===> Extracting for CheckM-1.0.13_1 => SHA256 Checksum OK for Ecogenomics-CheckM-v1.0.13_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for CheckM-1.0.13_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> CheckM-1.0.13_1 depends on package: py36-setuptools>0 - not found ===> Installing existing package /packages/All/py36-setuptools-41.0.1.txz Installing py36-setuptools-41.0.1... `-- Installing python36-3.6.9... | `-- Installing expat-2.2.6_1... | `-- Extracting expat-2.2.6_1: .......... done | `-- Installing gettext-runtime-0.20.1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | `-- Extracting gettext-runtime-0.20.1: .......... done | `-- Installing libffi-3.2.1_3... | `-- Extracting libffi-3.2.1_3: .......... done | `-- Installing libressl-2.9.2... | `-- Extracting libressl-2.9.2: .......... done | `-- Installing ncurses-6.1.20190525... | `-- Extracting ncurses-6.1.20190525: .......... done | `-- Installing readline-8.0.0... | `-- Extracting readline-8.0.0: .......... done `-- Extracting python36-3.6.9: .......... done Extracting py36-setuptools-41.0.1: .......... done Message from python36-3.6.9: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== ===> CheckM-1.0.13_1 depends on package: py36-setuptools>0 - found ===> Returning to build of CheckM-1.0.13_1 ===> CheckM-1.0.13_1 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for CheckM-1.0.13_1 running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for CheckM-1.0.13_1 running build running build_py creating build creating build/lib creating build/lib/checkm copying checkm/fileEntity.py -> build/lib/checkm copying checkm/treeParser.py -> build/lib/checkm copying checkm/profile.py -> build/lib/checkm copying checkm/binTools.py -> build/lib/checkm copying checkm/manifestManager.py -> build/lib/checkm copying checkm/__init__.py -> build/lib/checkm copying checkm/binComparer.py -> build/lib/checkm copying checkm/hmmerModelParser.py -> build/lib/checkm copying checkm/pplacer.py -> build/lib/checkm copying checkm/merger.py -> build/lib/checkm copying checkm/common.py -> build/lib/checkm copying checkm/main.py -> build/lib/checkm copying checkm/prodigal.py -> build/lib/checkm copying checkm/markerGeneFinder.py -> build/lib/checkm copying checkm/timeKeeper.py -> build/lib/checkm copying checkm/hmmer.py -> build/lib/checkm copying checkm/taxonParser.py -> build/lib/checkm copying checkm/genomicSignatures.py -> build/lib/checkm copying checkm/binUnion.py -> build/lib/checkm copying checkm/markerSets.py -> build/lib/checkm copying checkm/coverageWindows.py -> build/lib/checkm copying checkm/prettytable.py -> build/lib/checkm copying checkm/customHelpFormatter.py -> build/lib/checkm copying checkm/hmmerAligner.py -> build/lib/checkm copying checkm/unbinned.py -> build/lib/checkm copying checkm/binStatistics.py -> build/lib/checkm copying checkm/aminoAcidIdentity.py -> build/lib/checkm copying checkm/defaultValues.py -> build/lib/checkm copying checkm/ssuFinder.py -> build/lib/checkm copying checkm/PCA.py -> build/lib/checkm copying checkm/resultsParser.py -> build/lib/checkm copying checkm/uniqueMarkers.py -> build/lib/checkm copying checkm/coverage.py -> build/lib/checkm copying checkm/checkmData.py -> build/lib/checkm creating build/lib/checkm/plot copying checkm/plot/gcPlots.py -> build/lib/checkm/plot copying checkm/plot/codingDensityPlots.py -> build/lib/checkm/plot copying checkm/plot/lengthHistogram.py -> build/lib/checkm/plot copying checkm/plot/__init__.py -> build/lib/checkm/plot copying checkm/plot/parallelCoordPlot.py -> build/lib/checkm/plot copying checkm/plot/binQAPlot.py -> build/lib/checkm/plot copying checkm/plot/tetraDistPlots.py -> build/lib/checkm/plot copying checkm/plot/distributionPlots.py -> build/lib/checkm/plot copying checkm/plot/pcaPlot.py -> build/lib/checkm/plot copying checkm/plot/cumulativeLengthPlot.py -> build/lib/checkm/plot copying checkm/plot/AbstractPlot.py -> build/lib/checkm/plot copying checkm/plot/nxPlot.py -> build/lib/checkm/plot copying checkm/plot/gcBiasPlots.py -> build/lib/checkm/plot copying checkm/plot/markerGenePosPlot.py -> build/lib/checkm/plot creating build/lib/checkm/test copying checkm/test/test_aminoAcidIdentity.py -> build/lib/checkm/test copying checkm/test/test_binStatistics.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_markerSets.py -> build/lib/checkm/test copying checkm/test/test_genomicSignatures.py -> build/lib/checkm/test copying checkm/test/__init__.py -> build/lib/checkm/test copying checkm/test/test_seqUtils.py -> build/lib/checkm/test creating 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/__init__.py -> build/lib/checkm/util copying checkm/util/taxonomyUtils.py -> build/lib/checkm/util copying checkm/util/pfam.py -> build/lib/checkm/util copying checkm/VERSION -> build/lib/checkm copying checkm/DATA_CONFIG -> build/lib/checkm running build_scripts creating build/scripts-3.6 copying and adjusting bin/checkm -> build/scripts-3.6 changing mode of build/scripts-3.6/checkm from 644 to 755 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> CheckM-1.0.13_1 depends on package: py36-numpy>0 - not found ===> Installing existing package /packages/All/py36-numpy-1.16.4,1.txz Installing py36-numpy-1.16.4,1... `-- Installing gcc8-8.3.0_2... | `-- Installing binutils-2.32_1,1... | `-- Extracting binutils-2.32_1,1: .......... done | `-- Installing gmp-6.1.2_1... | `-- Extracting gmp-6.1.2_1: .......... done | `-- Installing mpc-1.1.0_2... | | `-- Installing mpfr-4.0.2... | | `-- Extracting mpfr-4.0.2: .......... done | `-- Extracting mpc-1.1.0_2: ......... done `-- Extracting gcc8-8.3.0_2: .......... done `-- Installing openblas-0.2.20_8,1... `-- Extracting openblas-0.2.20_8,1: ......... done `-- Installing suitesparse-5.2.0_3... | `-- Installing lapack-3.5.0_7... | | `-- Installing blas-3.5.0_5... | | `-- Extracting blas-3.5.0_5: ....... done | `-- Extracting lapack-3.5.0_7: .......... done | `-- Installing metis-5.1.0_7... | `-- Extracting metis-5.1.0_7: .......... done `-- Extracting suitesparse-5.2.0_3: .......... done Extracting py36-numpy-1.16.4,1: .......... done Message from gcc8-8.3.0_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/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from metis-5.1.0_7: ===> NOTICE: The metis 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> CheckM-1.0.13_1 depends on package: py36-numpy>0 - found ===> Returning to build of CheckM-1.0.13_1 ===> CheckM-1.0.13_1 depends on package: py36-DendroPy>=4.0.0 - not found ===> Installing existing package /packages/All/py36-DendroPy-4.4.0.txz Installing py36-DendroPy-4.4.0... Extracting py36-DendroPy-4.4.0: .......... done Message from py36-DendroPy-4.4.0: ************************************************************************ 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. ************************************************************************ ===> CheckM-1.0.13_1 depends on package: py36-DendroPy>=4.0.0 - found ===> Returning to build of CheckM-1.0.13_1 ===> CheckM-1.0.13_1 depends on package: py36-matplotlib>=1.3.1 - not found ===> Installing existing package /packages/All/py36-matplotlib-2.2.4.txz Installing py36-matplotlib-2.2.4... `-- Installing fontconfig-2.12.6,1... | `-- Installing freetype2-2.10.0... | `-- Extracting freetype2-2.10.0: .......... done `-- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded `-- Installing png-1.6.37... `-- Extracting png-1.6.37: .......... done `-- Installing py36-cycler-0.10.0... | `-- Installing py36-six-1.12.0... | `-- Extracting py36-six-1.12.0: .......... done `-- Extracting py36-cycler-0.10.0: .......... done `-- Installing py36-dateutil-2.8.0... `-- Extracting py36-dateutil-2.8.0: .......... done `-- Installing py36-kiwisolver-1.1.0... `-- Extracting py36-kiwisolver-1.1.0: ......... done `-- Installing py36-pyparsing-2.4.0... `-- Extracting py36-pyparsing-2.4.0: .......... done `-- Installing py36-pytz-2019.1,1... `-- Extracting py36-pytz-2019.1,1: .......... done `-- Installing py36-tkinter-3.6.9_6... | `-- Installing tcl86-8.6.9_1... | `-- Extracting tcl86-8.6.9_1: .......... done | `-- Installing tk86-8.6.9_1... | | `-- Installing libX11-1.6.8,1... | | `-- Installing libXau-1.0.9... | | `-- Extracting libXau-1.0.9: .......... done | | `-- Installing libXdmcp-1.1.3... | | | `-- Installing xorgproto-2019.1... | | | `-- Extracting xorgproto-2019.1: .......... done | | `-- Extracting libXdmcp-1.1.3: ......... done | | `-- Installing libxcb-1.13.1... | | | `-- Installing libpthread-stubs-0.4... | | | `-- Extracting libpthread-stubs-0.4: .... done | | | `-- Installing libxml2-2.9.9... | | | `-- Extracting libxml2-2.9.9: .......... done | | `-- Extracting libxcb-1.13.1: .......... done | | `-- Extracting libX11-1.6.8,1: .......... done | | `-- Installing libXScrnSaver-1.2.3_2... | | `-- Installing libXext-1.3.4,1... | | `-- Extracting libXext-1.3.4,1: .......... done | | `-- Extracting libXScrnSaver-1.2.3_2: .......... done | | `-- Installing libXft-2.3.2_3... | | `-- Installing libXrender-0.9.10_2... | | `-- Extracting libXrender-0.9.10_2: .......... done | | `-- Extracting libXft-2.3.2_3: .......... done | `-- Extracting tk86-8.6.9_1: .......... done `-- Extracting py36-tkinter-3.6.9_6: ........ done `-- Installing py36-tornado-5.1.1... `-- Extracting py36-tornado-5.1.1: .......... done Extracting py36-matplotlib-2.2.4: .......... done Message from freetype2-2.10.0: 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. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was installed). ===> CheckM-1.0.13_1 depends on package: py36-matplotlib>=1.3.1 - found ===> Returning to build of CheckM-1.0.13_1 ===> CheckM-1.0.13_1 depends on package: py36-pysam>=0.8.3 - not found ===> Installing existing package /packages/All/py36-pysam-0.15.2.txz Installing py36-pysam-0.15.2... `-- Installing py36-cython-0.29_1... `-- Extracting py36-cython-0.29_1: .......... done Extracting py36-pysam-0.15.2: .......... done ===> CheckM-1.0.13_1 depends on package: py36-pysam>=0.8.3 - found ===> Returning to build of CheckM-1.0.13_1 ===> CheckM-1.0.13_1 depends on package: py36-scipy>=0.9.0 - not found ===> Installing existing package /packages/All/py36-scipy-1.2.2.txz Installing py36-scipy-1.2.2... Extracting py36-scipy-1.2.2: .......... done ===> CheckM-1.0.13_1 depends on package: py36-scipy>=0.9.0 - found ===> Returning to build of CheckM-1.0.13_1 ===> CheckM-1.0.13_1 depends on package: py36-setuptools>0 - found ===> CheckM-1.0.13_1 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for CheckM-1.0.13_1 ===> Generating temporary packing list running install running build running build_py running build_scripts running install_lib creating /construction/biology/checkm/stage/usr/local/lib/python3.6 creating /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages creating /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/hmmer.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/markerGeneFinder.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/genomicSignatures.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/binComparer.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/binTools.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/main.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/prodigal.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/treeParser.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/fileEntity.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/timeKeeper.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/unbinned.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm creating /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test copying build/lib/checkm/test/test_ecoli.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test copying build/lib/checkm/test/test_aminoAcidIdentity.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test copying build/lib/checkm/test/test_binStatistics.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test copying build/lib/checkm/test/test_markerSets.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test copying build/lib/checkm/test/test_seqUtils.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test copying build/lib/checkm/test/__init__.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test copying build/lib/checkm/test/test_genomicSignatures.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test copying build/lib/checkm/test/test_taxonomyUtils.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test copying build/lib/checkm/merger.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/prettytable.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/profile.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/pplacer.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/checkmData.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/binUnion.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm creating /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/util copying build/lib/checkm/util/img.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/util copying build/lib/checkm/util/taxonomyUtils.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/util copying build/lib/checkm/util/pfam.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/util copying build/lib/checkm/util/seqUtils.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/util copying build/lib/checkm/util/__init__.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/util copying build/lib/checkm/resultsParser.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm creating /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/nxPlot.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/codingDensityPlots.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/gcBiasPlots.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/lengthHistogram.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/cumulativeLengthPlot.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/tetraDistPlots.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/__init__.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/pcaPlot.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/distributionPlots.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/AbstractPlot.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/markerGenePosPlot.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/binQAPlot.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/gcPlots.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/plot/parallelCoordPlot.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot copying build/lib/checkm/customHelpFormatter.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/ssuFinder.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/hmmerModelParser.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/binStatistics.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/DATA_CONFIG -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/markerSets.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/defaultValues.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/coverage.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/taxonParser.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/VERSION -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/manifestManager.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/PCA.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/common.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/hmmerAligner.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/aminoAcidIdentity.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/coverageWindows.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/uniqueMarkers.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm copying build/lib/checkm/__init__.py -> /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/hmmer.py to hmmer.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/markerGeneFinder.py to markerGeneFinder.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/genomicSignatures.py to genomicSignatures.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/binComparer.py to binComparer.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/binTools.py to binTools.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/main.py to main.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/prodigal.py to prodigal.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/treeParser.py to treeParser.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/fileEntity.py to fileEntity.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/timeKeeper.py to timeKeeper.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/unbinned.py to unbinned.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test/test_ecoli.py to test_ecoli.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test/test_aminoAcidIdentity.py to test_aminoAcidIdentity.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test/test_binStatistics.py to test_binStatistics.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test/test_markerSets.py to test_markerSets.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test/test_seqUtils.py to test_seqUtils.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test/test_genomicSignatures.py to test_genomicSignatures.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/test/test_taxonomyUtils.py to test_taxonomyUtils.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/merger.py to merger.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/prettytable.py to prettytable.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/profile.py to profile.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/pplacer.py to pplacer.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/checkmData.py to checkmData.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/binUnion.py to binUnion.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/util/img.py to img.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/util/taxonomyUtils.py to taxonomyUtils.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/util/pfam.py to pfam.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/util/seqUtils.py to seqUtils.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/util/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/resultsParser.py to resultsParser.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/nxPlot.py to nxPlot.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/codingDensityPlots.py to codingDensityPlots.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/gcBiasPlots.py to gcBiasPlots.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/lengthHistogram.py to lengthHistogram.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/cumulativeLengthPlot.py to cumulativeLengthPlot.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/tetraDistPlots.py to tetraDistPlots.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/pcaPlot.py to pcaPlot.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/distributionPlots.py to distributionPlots.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/AbstractPlot.py to AbstractPlot.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/markerGenePosPlot.py to markerGenePosPlot.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/binQAPlot.py to binQAPlot.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/gcPlots.py to gcPlots.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/plot/parallelCoordPlot.py to parallelCoordPlot.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/customHelpFormatter.py to customHelpFormatter.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/ssuFinder.py to ssuFinder.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/hmmerModelParser.py to hmmerModelParser.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/binStatistics.py to binStatistics.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/markerSets.py to markerSets.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/defaultValues.py to defaultValues.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/coverage.py to coverage.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/taxonParser.py to taxonParser.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/manifestManager.py to manifestManager.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/PCA.py to PCA.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/common.py to common.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/hmmerAligner.py to hmmerAligner.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/aminoAcidIdentity.py to aminoAcidIdentity.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/coverageWindows.py to coverageWindows.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/uniqueMarkers.py to uniqueMarkers.cpython-36.pyc byte-compiling /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm/__init__.py to __init__.cpython-36.pyc writing byte-compilation script '/tmp/tmp5bi1dlfs.py' /usr/local/bin/python3.6 /tmp/tmp5bi1dlfs.py File "/usr/local/lib/python3.6/site-packages/checkm/binTools.py", line 126 print ' [Warning] Sequence %s found multiple times in bin %s.' % (seqId, binId) ^ SyntaxError: invalid syntax Sorry: TabError: inconsistent use of tabs and spaces in indentation (test_ecoli.py, line 52) File "/usr/local/lib/python3.6/site-packages/checkm/checkmData.py", line 88 except IOError, e: ^ SyntaxError: invalid syntax File "/usr/local/lib/python3.6/site-packages/checkm/util/img.py", line 365 print '[BUG]: __genomeIdToClusterScaffold' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('[BUG]: __genomeIdToClusterScaffold')? File "/usr/local/lib/python3.6/site-packages/checkm/plot/codingDensityPlots.py", line 57 print 'Missing gene feature file (%s). This plot if not compatible with the --genes option.' % DefaultValues.PRODIGAL_GFF ^ SyntaxError: invalid syntax File "/usr/local/lib/python3.6/site-packages/checkm/coverage.py", line 174 print traceback.format_exc() ^ SyntaxError: invalid syntax File "/usr/local/lib/python3.6/site-packages/checkm/taxonParser.py", line 76 print '' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('')? File "/usr/local/lib/python3.6/site-packages/checkm/manifestManager.py", line 132 print "Error: failed to connect to server." ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Error: failed to connect to server.")? File "/usr/local/lib/python3.6/site-packages/checkm/coverageWindows.py", line 191 print '*****************' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('*****************')? File "/usr/local/lib/python3.6/site-packages/checkm/uniqueMarkers.py", line 54 print query_string ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(query_string)? removing /tmp/tmp5bi1dlfs.py running install_egg_info 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' File "/usr/local/lib/python3.6/site-packages/checkm/binTools.py", line 126 print ' [Warning] Sequence %s found multiple times in bin %s.' % (seqId, binId) ^ SyntaxError: invalid syntax Sorry: TabError: inconsistent use of tabs and spaces in indentation (test_ecoli.py, line 52) File "/usr/local/lib/python3.6/site-packages/checkm/checkmData.py", line 88 except IOError, e: ^ SyntaxError: invalid syntax File "/usr/local/lib/python3.6/site-packages/checkm/util/img.py", line 365 print '[BUG]: __genomeIdToClusterScaffold' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('[BUG]: __genomeIdToClusterScaffold')? File "/usr/local/lib/python3.6/site-packages/checkm/plot/codingDensityPlots.py", line 57 print 'Missing gene feature file (%s). This plot if not compatible with the --genes option.' % DefaultValues.PRODIGAL_GFF ^ SyntaxError: invalid syntax File "/usr/local/lib/python3.6/site-packages/checkm/coverage.py", line 174 print traceback.format_exc() ^ SyntaxError: invalid syntax File "/usr/local/lib/python3.6/site-packages/checkm/taxonParser.py", line 76 print '' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('')? File "/usr/local/lib/python3.6/site-packages/checkm/manifestManager.py", line 132 print "Error: failed to connect to server." ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Error: failed to connect to server.")? File "/usr/local/lib/python3.6/site-packages/checkm/coverageWindows.py", line 191 print '*****************' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('*****************')? File "/usr/local/lib/python3.6/site-packages/checkm/uniqueMarkers.py", line 54 print query_string ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(query_string)? warning: no files found matching '*.txt' under directory 'docs' writing manifest file 'checkm_genome.egg-info/SOURCES.txt' Copying checkm_genome.egg-info to /construction/biology/checkm/stage/usr/local/lib/python3.6/site-packages/checkm_genome-1.0.13-py3.6.egg-info running install_scripts copying build/scripts-3.6/checkm -> /construction/biology/checkm/stage/usr/local/bin changing mode of /construction/biology/checkm/stage/usr/local/bin/checkm to 755 writing list of installed files to '/construction/biology/checkm/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for CheckM-1.0.13_1 file sizes/checksums [174]: .. done packing files [174]: .. done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 24 JUL 2019 at 16:49:11 UTC Duration: 00:00:55