=> Building biology/py-gtfparse@py36 Started : Wednesday, 24 JUL 2019 at 17:29:08 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/py-gtfparse XDG_CONFIG_HOME=/construction/biology/py-gtfparse HOME=/construction/biology/py-gtfparse TMPDIR="/tmp" PATH=/construction/biology/py-gtfparse/.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/py-gtfparse XDG_CONFIG_HOME=/construction/biology/py-gtfparse HOME=/construction/biology/py-gtfparse TMPDIR="/tmp" PATH=/construction/biology/py-gtfparse/.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/py-gtfparse/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/gtfparse" EXAMPLESDIR="share/examples/gtfparse" DATADIR="share/gtfparse" WWWDIR="www/gtfparse" ETCDIR="etc/gtfparse" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gtfparse DOCSDIR=/usr/local/share/doc/gtfparse EXAMPLESDIR=/usr/local/share/examples/gtfparse WWWDIR=/usr/local/www/gtfparse ETCDIR=/usr/local/etc/gtfparse -------------------------------------------------- -- /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 APACHE20 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> py36-gtfparse-1.2.0_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 ===> py36-gtfparse-1.2.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py36-gtfparse-1.2.0_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by py36-gtfparse-1.2.0_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by py36-gtfparse-1.2.0_1 for building => SHA256 Checksum OK for gtfparse-1.2.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by py36-gtfparse-1.2.0_1 for building ===> Extracting for py36-gtfparse-1.2.0_1 => SHA256 Checksum OK for gtfparse-1.2.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py36-gtfparse-1.2.0_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py36-gtfparse-1.2.0_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 =========================================================================== ===> py36-gtfparse-1.2.0_1 depends on package: py36-setuptools>0 - found ===> Returning to build of py36-gtfparse-1.2.0_1 ===> py36-gtfparse-1.2.0_1 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py36-gtfparse-1.2.0_1 No module named 'pypandoc' Failed to convert README.md from Markdown to reStructuredText running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for py36-gtfparse-1.2.0_1 No module named 'pypandoc' Failed to convert README.md from Markdown to reStructuredText running build running build_py creating build creating build/lib creating build/lib/gtfparse copying gtfparse/required_columns.py -> build/lib/gtfparse copying gtfparse/read_gtf.py -> build/lib/gtfparse copying gtfparse/__init__.py -> build/lib/gtfparse copying gtfparse/attribute_parsing.py -> build/lib/gtfparse copying gtfparse/parsing_error.py -> build/lib/gtfparse copying gtfparse/create_missing_features.py -> build/lib/gtfparse -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> py36-gtfparse-1.2.0_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 ===> py36-gtfparse-1.2.0_1 depends on package: py36-numpy>0 - found ===> Returning to build of py36-gtfparse-1.2.0_1 ===> py36-gtfparse-1.2.0_1 depends on package: py36-pandas>=0.15 - not found ===> Installing existing package /packages/All/py36-pandas-0.24.2.txz Installing py36-pandas-0.24.2... `-- Installing py36-bottleneck-1.2.1_4... `-- Extracting py36-bottleneck-1.2.1_4: .......... done `-- Installing py36-dateutil-2.8.0... | `-- Installing py36-six-1.12.0... | `-- Extracting py36-six-1.12.0: .......... done `-- Extracting py36-dateutil-2.8.0: .......... done `-- Installing py36-numexpr-2.6.9... `-- Extracting py36-numexpr-2.6.9: .......... done `-- Installing py36-pytz-2019.1,1... `-- Extracting py36-pytz-2019.1,1: .......... done `-- Installing py36-sqlite3-3.6.9_7... | `-- Installing sqlite3-3.29.0... | `-- Extracting sqlite3-3.29.0: .......... done `-- Extracting py36-sqlite3-3.6.9_7: ........ done Extracting py36-pandas-0.24.2: .......... done Message from py36-pandas-0.24.2: === Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. === ===> py36-gtfparse-1.2.0_1 depends on package: py36-pandas>=0.15 - found ===> Returning to build of py36-gtfparse-1.2.0_1 ===> py36-gtfparse-1.2.0_1 depends on package: py36-setuptools>0 - found ===> py36-gtfparse-1.2.0_1 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py36-gtfparse-1.2.0_1 ===> Generating temporary packing list No module named 'pypandoc' Failed to convert README.md from Markdown to reStructuredText running install running build running build_py running install_lib creating /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6 creating /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages creating /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse copying build/lib/gtfparse/required_columns.py -> /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse copying build/lib/gtfparse/__init__.py -> /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse copying build/lib/gtfparse/create_missing_features.py -> /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse copying build/lib/gtfparse/read_gtf.py -> /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse copying build/lib/gtfparse/attribute_parsing.py -> /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse copying build/lib/gtfparse/parsing_error.py -> /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse byte-compiling /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse/required_columns.py to required_columns.cpython-36.pyc byte-compiling /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse/create_missing_features.py to create_missing_features.cpython-36.pyc byte-compiling /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse/read_gtf.py to read_gtf.cpython-36.pyc byte-compiling /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse/attribute_parsing.py to attribute_parsing.cpython-36.pyc byte-compiling /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse/parsing_error.py to parsing_error.cpython-36.pyc writing byte-compilation script '/tmp/tmpjdjenm31.py' /usr/local/bin/python3.6 /tmp/tmpjdjenm31.py removing /tmp/tmpjdjenm31.py running install_egg_info running egg_info writing gtfparse.egg-info/PKG-INFO writing dependency_links to gtfparse.egg-info/dependency_links.txt writing requirements to gtfparse.egg-info/requires.txt writing top-level names to gtfparse.egg-info/top_level.txt reading manifest file 'gtfparse.egg-info/SOURCES.txt' writing manifest file 'gtfparse.egg-info/SOURCES.txt' Copying gtfparse.egg-info to /construction/biology/py-gtfparse/stage/usr/local/lib/python3.6/site-packages/gtfparse-1.2.0-py3.6.egg-info running install_scripts writing list of installed files to '/construction/biology/py-gtfparse/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for py36-gtfparse-1.2.0_1 file sizes/checksums [26]: . done packing files [26]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 24 JUL 2019 at 17:29:40 UTC Duration: 00:00:31