=> Building biology/prodigy-lig Started : Thursday, 7 MAR 2019 at 18:28:34 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 -------------------------------------------------- MAKE=gmake PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/construction/biology/prodigy-lig XDG_CONFIG_HOME=/construction/biology/prodigy-lig HOME=/construction/biology/prodigy-lig TMPDIR="/tmp" PATH=/construction/biology/prodigy-lig/.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/prodigy-lig XDG_CONFIG_HOME=/construction/biology/prodigy-lig HOME=/construction/biology/prodigy-lig TMPDIR="/tmp" PATH=/construction/biology/prodigy-lig/.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/prodigy-lig/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/prodigy-lig" EXAMPLESDIR="share/examples/prodigy-lig" DATADIR="share/prodigy-lig" WWWDIR="www/prodigy-lig" ETCDIR="etc/prodigy-lig" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/prodigy-lig DOCSDIR=/usr/local/share/doc/prodigy-lig EXAMPLESDIR=/usr/local/share/examples/prodigy-lig WWWDIR=/usr/local/www/prodigy-lig ETCDIR=/usr/local/etc/prodigy-lig -------------------------------------------------- -- /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 APACHE20 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> prodigy-lig-1.0.0.3 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 ===> prodigy-lig-1.0.0.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of prodigy-lig-1.0.0.3 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License APACHE20 accepted by the user => haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/haddocking/prodigy-lig/tar.gz/v1.0.0-3-g152ac59?dummy=/haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz fetch: https://codeload.github.com/haddocking/prodigy-lig/tar.gz/v1.0.0-3-g152ac59?dummy=/haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz: size unknown fetch: https://codeload.github.com/haddocking/prodigy-lig/tar.gz/v1.0.0-3-g152ac59?dummy=/haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz: size of remote file is not known haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz -1 B 0 Bps ===> Fetching all distfiles required by prodigy-lig-1.0.0.3 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by prodigy-lig-1.0.0.3 for building => SHA256 Checksum OK for haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by prodigy-lig-1.0.0.3 for building ===> Extracting for prodigy-lig-1.0.0.3 => SHA256 Checksum OK for haddocking-prodigy-lig-v1.0.0-3-g152ac59_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for prodigy-lig-1.0.0.3 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> prodigy-lig-1.0.0.3 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... | | `-- 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 | `-- 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 py36-setuptools-40.8.0... | `-- Installing python36-3.6.8... | | `-- Installing expat-2.2.6_1... | | `-- Extracting expat-2.2.6_1: .......... 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 `-- 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 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. ******************************************************************* 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 ===> prodigy-lig-1.0.0.3 depends on package: py36-numpy>0 - found ===> Returning to build of prodigy-lig-1.0.0.3 ===> prodigy-lig-1.0.0.3 depends on package: py36-biopython>0 - not found ===> Installing existing package /packages/All/py36-biopython-1.73.txz Installing py36-biopython-1.73... `-- Installing py36-reportlab-3.5.13... | `-- Installing adobe-cmaps-20051217_3... | | `-- Installing fontconfig-2.12.6,1... | | `-- Installing freetype2-2.9.1... | | `-- Extracting freetype2-2.9.1: .......... 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 mkfontdir-1.0.7... | | `-- Installing mkfontscale-1.1.3_2... | | | `-- Installing libfontenc-1.1.4... | | | `-- Extracting libfontenc-1.1.4: ......... done | | `-- Extracting mkfontscale-1.1.3_2: ..... done | | `-- Extracting mkfontdir-1.0.7: ..... done | `-- Extracting adobe-cmaps-20051217_3: .......... done | `-- Installing py36-pillow-5.3.0... | | `-- Installing jpeg-turbo-2.0.2... | | `-- Extracting jpeg-turbo-2.0.2: .......... done | | `-- Installing openjpeg-2.3.0_3... | | `-- Installing lcms2-2.9... | | | `-- Installing tiff-4.0.10... | | | `-- Installing jbigkit-2.1_1... | | | `-- Extracting jbigkit-2.1_1: .......... done | | | `-- Extracting tiff-4.0.10: .......... done | | `-- Extracting lcms2-2.9: .......... done | | `-- Installing png-1.6.36... | | `-- Extracting png-1.6.36: .......... done | | `-- Extracting openjpeg-2.3.0_3: .......... done | | `-- Installing py36-tkinter-3.6.8_6... | | `-- Installing tcl86-8.6.9_1... | | `-- Extracting tcl86-8.6.9_1: .......... done | | `-- Installing tk86-8.6.9_1... | | | `-- Installing libX11-1.6.7,1... | | | `-- Installing libXau-1.0.8_5... | | | `-- Extracting libXau-1.0.8_5: .......... done | | | `-- Installing libXdmcp-1.1.2_2... | | | | `-- Installing xorgproto-2018.4... | | | | `-- Extracting xorgproto-2018.4: .......... done | | | `-- Extracting libXdmcp-1.1.2_2: ......... done | | | `-- Installing libxcb-1.13.1... | | | | `-- Installing libpthread-stubs-0.4... | | | | `-- Extracting libpthread-stubs-0.4: .... done | | | | `-- Installing libxml2-2.9.8... | | | | `-- Extracting libxml2-2.9.8: .......... done | | | `-- Extracting libxcb-1.13.1: .......... done | | | `-- Extracting libX11-1.6.7,1: .......... done | | | `-- Installing libXScrnSaver-1.2.3_2... | | | `-- Installing libXext-1.3.3_3,1... | | | `-- Extracting libXext-1.3.3_3,1: .......... 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-3.6.8_6: ........ done | | `-- Installing webp-1.0.2... | | `-- Installing giflib-5.1.4... | | `-- Extracting giflib-5.1.4: .......... done | | `-- Extracting webp-1.0.2: .......... done | `-- Extracting py36-pillow-5.3.0: .......... done `-- Extracting py36-reportlab-3.5.13: .......... done Extracting py36-biopython-1.73: .......... done Message from freetype2-2.9.1: 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/ft2-toc.html, if documentation was installed). ===> prodigy-lig-1.0.0.3 depends on package: py36-biopython>0 - found ===> Returning to build of prodigy-lig-1.0.0.3 ===> prodigy-lig-1.0.0.3 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... Extracting gmake-4.2.1_3: .......... done ===> prodigy-lig-1.0.0.3 depends on executable: gmake - found ===> Returning to build of prodigy-lig-1.0.0.3 ===> prodigy-lig-1.0.0.3 depends on package: py36-setuptools>0 - found ===> prodigy-lig-1.0.0.3 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for prodigy-lig-1.0.0.3 running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for prodigy-lig-1.0.0.3 running build running build_py creating build creating build/lib creating build/lib/prodigy_lig copying prodigy_lig/prodigy_lig.py -> build/lib/prodigy_lig copying prodigy_lig/__init__.py -> build/lib/prodigy_lig -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> prodigy-lig-1.0.0.3 depends on package: py36-setuptools>0 - found ===> prodigy-lig-1.0.0.3 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for prodigy-lig-1.0.0.3 ===> Generating temporary packing list running install running build running build_py running install_lib creating /construction/biology/prodigy-lig/stage/usr/local/lib/python3.6 creating /construction/biology/prodigy-lig/stage/usr/local/lib/python3.6/site-packages creating /construction/biology/prodigy-lig/stage/usr/local/lib/python3.6/site-packages/prodigy_lig copying build/lib/prodigy_lig/__init__.py -> /construction/biology/prodigy-lig/stage/usr/local/lib/python3.6/site-packages/prodigy_lig copying build/lib/prodigy_lig/prodigy_lig.py -> /construction/biology/prodigy-lig/stage/usr/local/lib/python3.6/site-packages/prodigy_lig byte-compiling /construction/biology/prodigy-lig/stage/usr/local/lib/python3.6/site-packages/prodigy_lig/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/biology/prodigy-lig/stage/usr/local/lib/python3.6/site-packages/prodigy_lig/prodigy_lig.py to prodigy_lig.cpython-36.pyc writing byte-compilation script '/tmp/tmp8j5ma6jt.py' /usr/local/bin/python3.6 /tmp/tmp8j5ma6jt.py removing /tmp/tmp8j5ma6jt.py running install_egg_info running egg_info creating prodigy_lig.egg-info writing prodigy_lig.egg-info/PKG-INFO writing dependency_links to prodigy_lig.egg-info/dependency_links.txt writing entry points to prodigy_lig.egg-info/entry_points.txt writing requirements to prodigy_lig.egg-info/requires.txt writing top-level names to prodigy_lig.egg-info/top_level.txt writing manifest file 'prodigy_lig.egg-info/SOURCES.txt' reading manifest file 'prodigy_lig.egg-info/SOURCES.txt' writing manifest file 'prodigy_lig.egg-info/SOURCES.txt' Copying prodigy_lig.egg-info to /construction/biology/prodigy-lig/stage/usr/local/lib/python3.6/site-packages/prodigy_lig-1.0.0-py3.6.egg-info running install_scripts Installing prodigy_lig script to /construction/biology/prodigy-lig/stage/usr/local/bin writing list of installed files to '/construction/biology/prodigy-lig/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for prodigy-lig-1.0.0.3 file sizes/checksums [17]: . done packing files [17]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 7 MAR 2019 at 18:29:31 UTC Duration: 00:00:57