=> Building biology/py-loompy@py36 Started : Thursday, 7 MAR 2019 at 18:36:11 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-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-loompy XDG_CONFIG_HOME=/construction/biology/py-loompy HOME=/construction/biology/py-loompy TMPDIR="/tmp" PATH=/construction/biology/py-loompy/.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-loompy XDG_CONFIG_HOME=/construction/biology/py-loompy HOME=/construction/biology/py-loompy TMPDIR="/tmp" PATH=/construction/biology/py-loompy/.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-loompy/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=opt-1.pyc PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/loompy" EXAMPLESDIR="share/examples/loompy" DATADIR="share/loompy" WWWDIR="www/loompy" ETCDIR="etc/loompy" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/loompy DOCSDIR=/usr/local/share/doc/loompy EXAMPLESDIR=/usr/local/share/examples/loompy WWWDIR=/usr/local/www/loompy ETCDIR=/usr/local/etc/loompy -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE 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=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License BSD2CLAUSE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> py36-loompy-2.0.17 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> py36-loompy-2.0.17 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py36-loompy-2.0.17 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSD2CLAUSE accepted by the user => loompy-2.0.17.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://files.pythonhosted.org/packages/source/l/loompy/loompy-2.0.17.tar.gz loompy-2.0.17.tar.gz 31 kB 0 Bps ===> Fetching all distfiles required by py36-loompy-2.0.17 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by py36-loompy-2.0.17 for building => SHA256 Checksum OK for loompy-2.0.17.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by py36-loompy-2.0.17 for building ===> Extracting for py36-loompy-2.0.17 => SHA256 Checksum OK for loompy-2.0.17.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py36-loompy-2.0.17 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py36-loompy-2.0.17 depends on package: py36-setuptools>0 - not found ===> Installing existing package /packages/All/py36-setuptools-40.8.0.txz Installing py36-setuptools-40.8.0... `-- Installing python36-3.6.8... | `-- Installing expat-2.2.6_1... | `-- Extracting expat-2.2.6_1: .......... done | `-- Installing gettext-runtime-0.19.8.1_2... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done | `-- Installing libffi-3.2.1_3... | `-- Extracting libffi-3.2.1_3: .......... done | `-- Installing libressl-2.8.3... | `-- Extracting libressl-2.8.3: .......... done | `-- Installing ncurses-6.1.20190112... | `-- Extracting ncurses-6.1.20190112: .......... done | `-- Installing readline-7.0.5... | `-- Extracting readline-7.0.5: .......... done `-- Extracting python36-3.6.8: .......... done Extracting py36-setuptools-40.8.0: .......... done Message from python36-3.6.8: =========================================================================== 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 =========================================================================== Message from py36-setuptools-40.8.0: ******************************************************************* Only /usr/local/bin/easy_install-3.6 script has been installed since Python 3.6 is not the default Python version. ******************************************************************* ===> py36-loompy-2.0.17 depends on package: py36-setuptools>0 - found ===> Returning to build of py36-loompy-2.0.17 ===> py36-loompy-2.0.17 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py36-loompy-2.0.17 running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for py36-loompy-2.0.17 running build running build_py creating build creating build/lib creating build/lib/loompy copying loompy/loom_validator.py -> build/lib/loompy copying loompy/layer_manager.py -> build/lib/loompy copying loompy/loom_view.py -> build/lib/loompy copying loompy/__init__.py -> build/lib/loompy copying loompy/to_html.py -> build/lib/loompy copying loompy/view_manager.py -> build/lib/loompy copying loompy/normalize.py -> build/lib/loompy copying loompy/utils.py -> build/lib/loompy copying loompy/_version.py -> build/lib/loompy copying loompy/loom_layer.py -> build/lib/loompy copying loompy/file_attribute_manager.py -> build/lib/loompy copying loompy/graph_manager.py -> build/lib/loompy copying loompy/loompy.py -> build/lib/loompy copying loompy/attribute_manager.py -> build/lib/loompy creating build/lib/loompy/plotting copying loompy/plotting/__init__.py -> build/lib/loompy/plotting copying loompy/plotting/plot.py -> build/lib/loompy/plotting copying loompy/plotting/color.py -> build/lib/loompy/plotting -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> py36-loompy-2.0.17 depends on package: py36-numpy>0 - not found ===> Installing existing package /packages/All/py36-numpy-1.16.1,1.txz Installing py36-numpy-1.16.1,1... `-- Installing gcc5-5.5.0_6... | `-- Installing binutils-2.32,1... | `-- Extracting binutils-2.32,1: .......... 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 gcc5-5.5.0_6: .......... done `-- Installing openblas-0.2.20_7,1... `-- Extracting openblas-0.2.20_7,1: ......... done `-- Installing suitesparse-5.2.0_2... | `-- Installing lapack-3.5.0_6... | | `-- Installing blas-3.5.0_5... | | `-- Extracting blas-3.5.0_5: ....... done | `-- Extracting lapack-3.5.0_6: .......... done | `-- Installing metis-5.1.0_7... | `-- Extracting metis-5.1.0_7: .......... done `-- Extracting suitesparse-5.2.0_2: .......... done Extracting py36-numpy-1.16.1,1: .......... done Message from gcc5-5.5.0_6: 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/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unsupported by upstream. Use GCC 7 or newer instead.. 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-loompy-2.0.17 depends on package: py36-numpy>0 - found ===> Returning to build of py36-loompy-2.0.17 ===> py36-loompy-2.0.17 depends on package: py36-h5py>0 - not found ===> Installing existing package /packages/All/py36-h5py-2.9.0_1.txz Installing py36-h5py-2.9.0_1... `-- Installing hdf5-1.10.1_2... | `-- Installing hdf-szip-2.1.1... | `-- Extracting hdf-szip-2.1.1: .......... done `-- Extracting hdf5-1.10.1_2: .......... done `-- Installing py36-six-1.12.0... `-- Extracting py36-six-1.12.0: .......... done Extracting py36-h5py-2.9.0_1: .......... done ===> py36-loompy-2.0.17 depends on package: py36-h5py>0 - found ===> Returning to build of py36-loompy-2.0.17 ===> py36-loompy-2.0.17 depends on package: py36-pandas>0 - not found ===> Installing existing package /packages/All/py36-pandas-0.24.0.txz Installing py36-pandas-0.24.0... `-- Installing py36-bottleneck-1.2.1_4... `-- Extracting py36-bottleneck-1.2.1_4: .......... done `-- Installing py36-dateutil-2.7.3... `-- Extracting py36-dateutil-2.7.3: .......... done `-- Installing py36-numexpr-2.6.9... `-- Extracting py36-numexpr-2.6.9: .......... done `-- Installing py36-pytz-2018.9,1... `-- Extracting py36-pytz-2018.9,1: .......... done `-- Installing py36-sqlite3-3.6.8_7... | `-- Installing sqlite3-3.27.1... | `-- Extracting sqlite3-3.27.1: .......... done `-- Extracting py36-sqlite3-3.6.8_7: ........ done Extracting py36-pandas-0.24.0: .......... done Message from py36-pandas-0.24.0: === Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. === ===> py36-loompy-2.0.17 depends on package: py36-pandas>0 - found ===> Returning to build of py36-loompy-2.0.17 ===> py36-loompy-2.0.17 depends on package: py36-scipy>0 - not found ===> Installing existing package /packages/All/py36-scipy-1.2.0.txz Installing py36-scipy-1.2.0... Extracting py36-scipy-1.2.0: .......... done ===> py36-loompy-2.0.17 depends on package: py36-scipy>0 - found ===> Returning to build of py36-loompy-2.0.17 ===> py36-loompy-2.0.17 depends on package: py36-setuptools>0 - found ===> py36-loompy-2.0.17 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py36-loompy-2.0.17 ===> Generating temporary packing list running install running build running build_py running install_lib creating /construction/biology/py-loompy/stage/usr/local/lib/python3.6 creating /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages creating /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/layer_manager.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/loom_view.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/graph_manager.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/view_manager.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/to_html.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/file_attribute_manager.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/loompy.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/_version.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/normalize.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/__init__.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/loom_validator.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy creating /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/plotting copying build/lib/loompy/plotting/color.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/plotting copying build/lib/loompy/plotting/__init__.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/plotting copying build/lib/loompy/plotting/plot.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/plotting copying build/lib/loompy/utils.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/loom_layer.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy copying build/lib/loompy/attribute_manager.py -> /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/layer_manager.py to layer_manager.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/loom_view.py to loom_view.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/graph_manager.py to graph_manager.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/view_manager.py to view_manager.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/to_html.py to to_html.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/file_attribute_manager.py to file_attribute_manager.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/loompy.py to loompy.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/_version.py to _version.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/normalize.py to normalize.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/loom_validator.py to loom_validator.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/plotting/color.py to color.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/plotting/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/plotting/plot.py to plot.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/utils.py to utils.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/loom_layer.py to loom_layer.cpython-36.pyc byte-compiling /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy/attribute_manager.py to attribute_manager.cpython-36.pyc writing byte-compilation script '/tmp/tmpdx2jq06z.py' /usr/local/bin/python3.6 /tmp/tmpdx2jq06z.py removing /tmp/tmpdx2jq06z.py running install_egg_info running egg_info writing loompy.egg-info/PKG-INFO writing dependency_links to loompy.egg-info/dependency_links.txt writing requirements to loompy.egg-info/requires.txt writing top-level names to loompy.egg-info/top_level.txt reading manifest file 'loompy.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'loompy.egg-info/SOURCES.txt' Copying loompy.egg-info to /construction/biology/py-loompy/stage/usr/local/lib/python3.6/site-packages/loompy-2.0.17-py3.6.egg-info running install_scripts writing list of installed files to '/construction/biology/py-loompy/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for py36-loompy-2.0.17 file sizes/checksums [59]: . done packing files [59]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 7 MAR 2019 at 18:36:49 UTC Duration: 00:00:37