------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 FLAVOR=py39 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/construction/biology/py-gffutils XDG_CONFIG_HOME=/construction/biology/py-gffutils XDG_CACHE_HOME=/construction/biology/py-gffutils/.cache HOME=/construction/biology/py-gffutils TMPDIR="/tmp" PATH=/construction/biology/py-gffutils/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-gffutils/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/py-gffutils XDG_CONFIG_HOME=/construction/biology/py-gffutils XDG_CACHE_HOME=/construction/biology/py-gffutils/.cache HOME=/construction/biology/py-gffutils TMPDIR="/tmp" PATH=/construction/biology/py-gffutils/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-gffutils/.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 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/py-gffutils/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/py39-gffutils" EXAMPLESDIR="share/examples/py39-gffutils" DATADIR="share/py39-gffutils" WWWDIR="www/py39-gffutils" ETCDIR="etc/py39-gffutils" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py39-gffutils DOCSDIR=/usr/local/share/doc/py39-gffutils EXAMPLESDIR=/usr/local/share/examples/py39-gffutils WWWDIR=/usr/local/www/py39-gffutils ETCDIR=/usr/local/etc/py39-gffutils SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/libffi-3.4.4.pkg Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/mpdecimal-2.5.1.pkg Installing /packages/All/ncurses-6.4.pkg ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/readline-8.2.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/python39-3.9.17.pkg ===== Message from python39-3.9.17: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 Installing /packages/All/py39-setuptools-63.1.0_1.pkg Installing /packages/All/ccache-3.7.12_4.pkg 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 gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. Installing /packages/All/py39-argcomplete-2.1.2.pkg Installing /packages/All/py39-argh-0.28.1_1.pkg Installing /packages/All/py39-six-1.16.0.pkg Installing /packages/All/py39-pyfaidx-0.5.9.5.pkg Installing /packages/All/py39-simplejson-3.18.4.pkg SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py39-gffutils-0.11.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py39-gffutils-0.11.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-gffutils-0.11.1 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py39-gffutils-0.11.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-gffutils-0.11.1 for building => SHA256 Checksum OK for gffutils-0.11.1.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py39-gffutils-0.11.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-gffutils-0.11.1 for building ===> Extracting for py39-gffutils-0.11.1 => SHA256 Checksum OK for gffutils-0.11.1.tar.gz. Extracted Memory Use: 9.61M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py39-gffutils-0.11.1 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py39-gffutils-0.11.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-gffutils-0.11.1 depends on file: /usr/local/bin/python3.9 - found ===> py39-gffutils-0.11.1 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py39-gffutils-0.11.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-gffutils-0.11.1 depends on file: /usr/local/bin/python3.9 - found ===> py39-gffutils-0.11.1 depends on file: /usr/local/bin/ccache - found ===> Configuring for py39-gffutils-0.11.1 /usr/local/lib/python3.9/site-packages/setuptools/dist.py:530: UserWarning: Normalizing ' 0.11.1' to '0.11.1' warnings.warn(tmpl.format(**locals())) running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py39-gffutils-0.11.1 /usr/local/lib/python3.9/site-packages/setuptools/dist.py:530: UserWarning: Normalizing ' 0.11.1' to '0.11.1' warnings.warn(tmpl.format(**locals())) running build running build_py creating build creating build/lib creating build/lib/gffutils copying gffutils/__init__.py -> build/lib/gffutils copying gffutils/attributes.py -> build/lib/gffutils copying gffutils/bins.py -> build/lib/gffutils copying gffutils/biopython_integration.py -> build/lib/gffutils copying gffutils/constants.py -> build/lib/gffutils copying gffutils/convert.py -> build/lib/gffutils copying gffutils/create.py -> build/lib/gffutils copying gffutils/exceptions.py -> build/lib/gffutils copying gffutils/feature.py -> build/lib/gffutils copying gffutils/gffwriter.py -> build/lib/gffutils copying gffutils/helpers.py -> build/lib/gffutils copying gffutils/inspect.py -> build/lib/gffutils copying gffutils/interface.py -> build/lib/gffutils copying gffutils/iterators.py -> build/lib/gffutils copying gffutils/merge_criteria.py -> build/lib/gffutils copying gffutils/parser.py -> build/lib/gffutils copying gffutils/pybedtools_integration.py -> build/lib/gffutils copying gffutils/version.py -> build/lib/gffutils creating build/lib/gffutils/scripts copying gffutils/scripts/gffutils-flybase-convert.py -> build/lib/gffutils/scripts creating build/lib/gffutils/test copying gffutils/test/__init__.py -> build/lib/gffutils/test copying gffutils/test/attr_test_cases.py -> build/lib/gffutils/test copying gffutils/test/expected.py -> build/lib/gffutils/test copying gffutils/test/feature_test.py -> build/lib/gffutils/test copying gffutils/test/helpers_test.py -> build/lib/gffutils/test copying gffutils/test/parser_test.py -> build/lib/gffutils/test copying gffutils/test/performance_evaluation.py -> build/lib/gffutils/test copying gffutils/test/synth_test_base.py -> build/lib/gffutils/test copying gffutils/test/test.py -> build/lib/gffutils/test copying gffutils/test/test_biopython_integration.py -> build/lib/gffutils/test copying gffutils/test/test_issues.py -> build/lib/gffutils/test copying gffutils/test/test_iterators.py -> build/lib/gffutils/test copying gffutils/test/test_merge.py -> build/lib/gffutils/test copying gffutils/test/test_merge_all.py -> build/lib/gffutils/test creating build/lib/gffutils/test/data copying gffutils/test/data/a.py -> build/lib/gffutils/test/data copying gffutils/test/data/F3-unique-3.v2.gff -> build/lib/gffutils/test/data copying gffutils/test/data/FBgn0031208.gff -> build/lib/gffutils/test/data copying gffutils/test/data/FBgn0031208.gtf -> build/lib/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> build/lib/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> build/lib/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> build/lib/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_ann_gff.txt -> build/lib/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> build/lib/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> build/lib/gffutils/test/data copying gffutils/test/data/dm6-chr2L.fa -> build/lib/gffutils/test/data copying gffutils/test/data/dm6-chr2L.fa.fai -> build/lib/gffutils/test/data copying gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> build/lib/gffutils/test/data copying gffutils/test/data/download-large-annotation-files.sh -> build/lib/gffutils/test/data copying gffutils/test/data/ensembl_gtf.txt -> build/lib/gffutils/test/data copying gffutils/test/data/gencode-v19.gtf -> build/lib/gffutils/test/data copying gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> build/lib/gffutils/test/data copying gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> build/lib/gffutils/test/data copying gffutils/test/data/gencode.vM8.chromsizes.txt -> build/lib/gffutils/test/data copying gffutils/test/data/gff_example1.gff3 -> build/lib/gffutils/test/data copying gffutils/test/data/gff_example1.gff3.gz -> build/lib/gffutils/test/data copying gffutils/test/data/glimmer_nokeyval.gff3 -> build/lib/gffutils/test/data copying gffutils/test/data/gms2_example.gff3 -> build/lib/gffutils/test/data copying gffutils/test/data/hybrid1.gff3 -> build/lib/gffutils/test/data copying gffutils/test/data/intro_docs_example.gff -> build/lib/gffutils/test/data copying gffutils/test/data/issue167.gff -> build/lib/gffutils/test/data copying gffutils/test/data/issue174.gtf -> build/lib/gffutils/test/data copying gffutils/test/data/issue181.gff -> build/lib/gffutils/test/data copying gffutils/test/data/issue_197.gff -> build/lib/gffutils/test/data copying gffutils/test/data/jgi_gff2.txt -> build/lib/gffutils/test/data copying gffutils/test/data/keep-order-test.gtf -> build/lib/gffutils/test/data copying gffutils/test/data/keyval_sep_in_attrs.gff -> build/lib/gffutils/test/data copying gffutils/test/data/mouse_extra_comma.gff3 -> build/lib/gffutils/test/data copying gffutils/test/data/ncbi_gff3.txt -> build/lib/gffutils/test/data copying gffutils/test/data/nonascii -> build/lib/gffutils/test/data copying gffutils/test/data/random-chr.gff -> build/lib/gffutils/test/data copying gffutils/test/data/sharr.gtf -> build/lib/gffutils/test/data copying gffutils/test/data/synthetic.gff3 -> build/lib/gffutils/test/data copying gffutils/test/data/unsanitized.gff -> build/lib/gffutils/test/data copying gffutils/test/data/wormbase_gff2.txt -> build/lib/gffutils/test/data copying gffutils/test/data/wormbase_gff2_alt.txt -> build/lib/gffutils/test/data running build_scripts creating build/scripts-3.9 copying and adjusting gffutils/scripts/gffutils-cli -> build/scripts-3.9 changing mode of build/scripts-3.9/gffutils-cli from 644 to 755 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py39-gffutils-0.11.1 depends on package: py39-argcomplete>=1.9.4 - found ===> py39-gffutils-0.11.1 depends on package: py39-argh>=0.26.2 - found ===> py39-gffutils-0.11.1 depends on package: py39-pyfaidx>=0.5.5.2 - found ===> py39-gffutils-0.11.1 depends on package: py39-simplejson>0 - found ===> py39-gffutils-0.11.1 depends on package: py39-six>=1.12.0 - found ===> py39-gffutils-0.11.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-gffutils-0.11.1 depends on file: /usr/local/bin/python3.9 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py39-gffutils-0.11.1 ===> py39-gffutils-0.11.1 depends on package: py39-argcomplete>=1.9.4 - found ===> py39-gffutils-0.11.1 depends on package: py39-argh>=0.26.2 - found ===> py39-gffutils-0.11.1 depends on package: py39-pyfaidx>=0.5.5.2 - found ===> py39-gffutils-0.11.1 depends on package: py39-simplejson>0 - found ===> py39-gffutils-0.11.1 depends on package: py39-six>=1.12.0 - found ===> py39-gffutils-0.11.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-gffutils-0.11.1 depends on file: /usr/local/bin/python3.9 - found ===> Generating temporary packing list /usr/local/lib/python3.9/site-packages/setuptools/dist.py:530: UserWarning: Normalizing ' 0.11.1' to '0.11.1' warnings.warn(tmpl.format(**locals())) running install /usr/local/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_scripts running install_lib creating /construction/biology/py-gffutils/stage/usr/local/lib/python3.9 creating /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages creating /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/__init__.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/attributes.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/bins.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/biopython_integration.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/constants.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/convert.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/create.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/exceptions.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/feature.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/gffwriter.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/helpers.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/inspect.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/interface.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/iterators.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/merge_criteria.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/parser.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/pybedtools_integration.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils copying build/lib/gffutils/version.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils creating /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/scripts copying build/lib/gffutils/scripts/gffutils-flybase-convert.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/scripts creating /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/__init__.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/attr_test_cases.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/expected.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/feature_test.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/helpers_test.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/parser_test.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/performance_evaluation.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/synth_test_base.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/test.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/test_biopython_integration.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/test_issues.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/test_iterators.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/test_merge.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test copying build/lib/gffutils/test/test_merge_all.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test creating /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/a.py -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/F3-unique-3.v2.gff -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/FBgn0031208.gff -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/FBgn0031208.gtf -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/c_elegans_WS199_ann_gff.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/dm6-chr2L.fa -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/dm6-chr2L.fa.fai -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/download-large-annotation-files.sh -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/ensembl_gtf.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/gencode-v19.gtf -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/gencode.vM8.chromsizes.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/gff_example1.gff3 -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/gff_example1.gff3.gz -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/glimmer_nokeyval.gff3 -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/gms2_example.gff3 -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/hybrid1.gff3 -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/intro_docs_example.gff -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/issue167.gff -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/issue174.gtf -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/issue181.gff -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/issue_197.gff -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/jgi_gff2.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/keep-order-test.gtf -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/keyval_sep_in_attrs.gff -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/mouse_extra_comma.gff3 -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/ncbi_gff3.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/nonascii -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/random-chr.gff -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/sharr.gtf -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/synthetic.gff3 -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/unsanitized.gff -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/wormbase_gff2.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data copying build/lib/gffutils/test/data/wormbase_gff2_alt.txt -> /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/attributes.py to attributes.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/bins.py to bins.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/biopython_integration.py to biopython_integration.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/constants.py to constants.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/convert.py to convert.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/create.py to create.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/exceptions.py to exceptions.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/feature.py to feature.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/gffwriter.py to gffwriter.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/helpers.py to helpers.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/inspect.py to inspect.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/interface.py to interface.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/iterators.py to iterators.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/merge_criteria.py to merge_criteria.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/parser.py to parser.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/pybedtools_integration.py to pybedtools_integration.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/version.py to version.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/scripts/gffutils-flybase-convert.py to gffutils-flybase-convert.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/attr_test_cases.py to attr_test_cases.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/expected.py to expected.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/feature_test.py to feature_test.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/helpers_test.py to helpers_test.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/parser_test.py to parser_test.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/performance_evaluation.py to performance_evaluation.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/synth_test_base.py to synth_test_base.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/test.py to test.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/test_biopython_integration.py to test_biopython_integration.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/test_issues.py to test_issues.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/test_iterators.py to test_iterators.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/test_merge.py to test_merge.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/test_merge_all.py to test_merge_all.cpython-39.pyc byte-compiling /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils/test/data/a.py to a.cpython-39.pyc writing byte-compilation script '/tmp/tmps5mrnab0.py' /usr/local/bin/python3.9 /tmp/tmps5mrnab0.py removing /tmp/tmps5mrnab0.py running install_egg_info running egg_info writing gffutils.egg-info/PKG-INFO writing dependency_links to gffutils.egg-info/dependency_links.txt writing requirements to gffutils.egg-info/requires.txt writing top-level names to gffutils.egg-info/top_level.txt reading manifest file 'gffutils.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.rst' under directory 'docs/source' warning: no files found matching '*.py' under directory 'docs/source' warning: no files found matching '*' under directory 'docs/source/images' warning: no files found matching 'docs/Makefile' warning: no files found matching 'docs/make.bat' warning: no files found matching 'gffutils/test/data/__init__.py' warning: no files found matching 'gffutils/test/data/t.py' adding license file 'LICENSE' writing manifest file 'gffutils.egg-info/SOURCES.txt' Copying gffutils.egg-info to /construction/biology/py-gffutils/stage/usr/local/lib/python3.9/site-packages/gffutils-0.11.1-py3.9.egg-info running install_scripts copying build/scripts-3.9/gffutils-cli -> /construction/biology/py-gffutils/stage/usr/local/bin changing mode of /construction/biology/py-gffutils/stage/usr/local/bin/gffutils-cli to 755 writing list of installed files to '/construction/biology/py-gffutils/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/gffutils-cli --> bin/gffutils-cli-3.9 Link: @bin/gffutils-cli --> bin/gffutils-cli-3.9 ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py39-gffutils-0.11.1 file sizes/checksums [149]: 0% file sizes/checksums [149]: 67% file sizes/checksums [149]: 100% Service unavailablepacking files [149]: 0% packing files [149]: 67% packing files [149]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:02 TOTAL TIME 00:00:15