------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/expat-2.2.8.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/libffi-3.2.1_3.txz Installing /packages/All/ncurses-6.1.20190525.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python27-2.7.18.txz ===== Message from python27-2.7.18: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter Installing /packages/All/py27-setuptools-44.0.0.txz ===== Message from py27-setuptools-44.0.0: -- Only /usr/local/bin/easy_install-2.7 script has been installed since Python 2.7 is not the default Python version. -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/metis-5.1.0_8.txz Installing /packages/All/tbb-2020.2.txz Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/mpfr-4.0.2.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/binutils-2.33.1_2,1.txz Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- 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. Installing /packages/All/openblas-0.3.9_2,1.txz Installing /packages/All/suitesparse-5.7.2_1.txz Installing /packages/All/py27-numpy-1.16.6,1.txz ===== Message from py27-numpy-1.16.6,1: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/freetype2-2.10.2.txz ===== Message from freetype2-2.10.2: -- 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. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was installed). Installing /packages/All/png-1.6.37.txz Installing /packages/All/fontconfig-2.13.92_2,1.txz Running fc-cache to build fontconfig cache... Font directories: /usr/local/share/fonts /usr/local/lib/X11/fonts /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 /packages/All/tcl86-8.6.10.txz Installing /packages/All/py27-six-1.14.0.txz ===== Message from py27-six-1.14.0: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-cycler-0.10.0.txz ===== Message from py27-cycler-0.10.0: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-dateutil-2.8.1.txz ===== Message from py27-dateutil-2.8.1: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-pytz-2020.1,1.txz ===== Message from py27-pytz-2020.1,1: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-pyparsing-2.4.7.txz ===== Message from py27-pyparsing-2.4.7: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-futures-3.3.0.txz ===== Message from py27-futures-3.3.0: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-singledispatch-3.4.0.3_1.txz ===== Message from py27-singledispatch-3.4.0.3_1: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-backports_abc-0.5.txz ===== Message from py27-backports_abc-0.5: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-tornado-5.1.1.txz ===== Message from py27-tornado-5.1.1: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-kiwisolver-1.1.0.txz ===== Message from py27-kiwisolver-1.1.0: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/libXau-1.0.9.txz Installing /packages/All/libxml2-2.9.10.txz Installing /packages/All/libpthread-stubs-0.4.txz Installing /packages/All/xorgproto-2020.1.txz Installing /packages/All/libXdmcp-1.1.3.txz Installing /packages/All/libxcb-1.13.1.txz Installing /packages/All/libX11-1.6.9_1,1.txz Installing /packages/All/libXext-1.3.4,1.txz Installing /packages/All/libXrender-0.9.10_2.txz Installing /packages/All/libXft-2.3.3.txz Installing /packages/All/libXScrnSaver-1.2.3_2.txz Installing /packages/All/tk86-8.6.10_1.txz Installing /packages/All/py27-tkinter-2.7.18_6.txz ===== Message from py27-tkinter-2.7.18_6: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-backports-1.txz ===== Message from py27-backports-1: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-backports.functools_lru_cache-1.5.txz ===== Message from py27-backports.functools_lru_cache-1.5: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-matplotlib-2.2.4_2.txz ===== Message from py27-matplotlib-2.2.4_2: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-scipy-1.2.2_1.txz ===== Message from py27-scipy-1.2.2_1: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/hdf-szip-2.1.1.txz Installing /packages/All/hdf5-1.10.6,1.txz Installing /packages/All/lzo2-2.10_1.txz Installing /packages/All/ucl-1.03_5.txz ===== Message from ucl-1.03_5: -- ===> NOTICE: The ucl 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 Installing /packages/All/py27-numexpr-2.7.1.txz ===== Message from py27-numexpr-2.7.1: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. Installing /packages/All/py27-tables-3.5.2_1.txz ===== Message from py27-tables-3.5.2_1: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:35 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- /!\ GroopM-0.3.4_2: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-08-15. SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> GroopM-0.3.4_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- /!\ GroopM-0.3.4_2: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-08-15. ===> GroopM-0.3.4_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by GroopM-0.3.4_2 for building SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- /!\ GroopM-0.3.4_2: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-08-15. ===> GroopM-0.3.4_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by GroopM-0.3.4_2 for building => SHA256 Checksum OK for GroopM-0.3.4.tar.gz. SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- /!\ GroopM-0.3.4_2: Makefile warnings, please consider fixing /!\ lang/python27 reached End of Life and will be removed on 2020-12-31, consider converting to a modern version of python ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-08-15. ===> GroopM-0.3.4_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by GroopM-0.3.4_2 for building ===> Extracting for GroopM-0.3.4_2 => SHA256 Checksum OK for GroopM-0.3.4.tar.gz. Extracted Memory Use: 0.65M SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for GroopM-0.3.4_2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> GroopM-0.3.4_2 depends on package: py27-setuptools>0 - found ===> GroopM-0.3.4_2 depends on file: /usr/local/bin/python2.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> GroopM-0.3.4_2 depends on package: py27-setuptools>0 - found ===> GroopM-0.3.4_2 depends on file: /usr/local/bin/python2.7 - found ===> Configuring for GroopM-0.3.4_2 running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for GroopM-0.3.4_2 running build running build_py creating build creating build/lib creating build/lib/groopm copying groopm/profileManager.py -> build/lib/groopm copying groopm/cluster.py -> build/lib/groopm copying groopm/torusMesh.py -> build/lib/groopm copying groopm/groopm.py -> build/lib/groopm copying groopm/bin.py -> build/lib/groopm copying groopm/groopmExceptions.py -> build/lib/groopm copying groopm/__init__.py -> build/lib/groopm copying groopm/som.py -> build/lib/groopm copying groopm/groopmUtils.py -> build/lib/groopm copying groopm/ellipsoid.py -> build/lib/groopm copying groopm/mstore.py -> build/lib/groopm copying groopm/PCA.py -> build/lib/groopm copying groopm/groopmTimekeeper.py -> build/lib/groopm copying groopm/rainbow.py -> build/lib/groopm copying groopm/binManager.py -> build/lib/groopm copying groopm/refine.py -> build/lib/groopm running build_scripts creating build/scripts-2.7 copying and adjusting bin/groopm -> build/scripts-2.7 changing mode of build/scripts-2.7/groopm from 644 to 755 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> GroopM-0.3.4_2 depends on package: py27-numpy>=1.16,1<1.19,1 - found ===> GroopM-0.3.4_2 depends on package: py27-matplotlib>=1.1.0 - found ===> GroopM-0.3.4_2 depends on package: py27-scipy>=0.10.1 - found ===> GroopM-0.3.4_2 depends on package: py27-tables>=2.3 - found ===> GroopM-0.3.4_2 depends on package: py27-setuptools>0 - found ===> GroopM-0.3.4_2 depends on file: /usr/local/bin/python2.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for GroopM-0.3.4_2 ===> GroopM-0.3.4_2 depends on package: py27-numpy>=1.16,1<1.19,1 - found ===> GroopM-0.3.4_2 depends on package: py27-matplotlib>=1.1.0 - found ===> GroopM-0.3.4_2 depends on package: py27-scipy>=0.10.1 - found ===> GroopM-0.3.4_2 depends on package: py27-tables>=2.3 - found ===> GroopM-0.3.4_2 depends on package: py27-setuptools>0 - found ===> GroopM-0.3.4_2 depends on file: /usr/local/bin/python2.7 - found ===> Generating temporary packing list running install running build running build_py running build_scripts running install_lib creating /construction/biology/groopm/stage/usr/local/lib/python2.7 creating /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages creating /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/refine.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/mstore.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/ellipsoid.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/__init__.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/som.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/groopm.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/profileManager.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/bin.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/groopmExceptions.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/torusMesh.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/groopmTimekeeper.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/cluster.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/rainbow.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/PCA.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/binManager.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/groopmUtils.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/refine.py to refine.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/mstore.py to mstore.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/ellipsoid.py to ellipsoid.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/__init__.py to __init__.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/som.py to som.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/groopm.py to groopm.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/profileManager.py to profileManager.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/bin.py to bin.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/groopmExceptions.py to groopmExceptions.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/torusMesh.py to torusMesh.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/groopmTimekeeper.py to groopmTimekeeper.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/cluster.py to cluster.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/rainbow.py to rainbow.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/PCA.py to PCA.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/binManager.py to binManager.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/groopmUtils.py to groopmUtils.pyc writing byte-compilation script '/tmp/tmpwEg4PU.py' /usr/local/bin/python2.7 -O /tmp/tmpwEg4PU.py removing /tmp/tmpwEg4PU.py running install_egg_info running egg_info creating GroopM.egg-info writing requirements to GroopM.egg-info/requires.txt writing GroopM.egg-info/PKG-INFO writing top-level names to GroopM.egg-info/top_level.txt writing dependency_links to GroopM.egg-info/dependency_links.txt writing manifest file 'GroopM.egg-info/SOURCES.txt' reading manifest file 'GroopM.egg-info/SOURCES.txt' writing manifest file 'GroopM.egg-info/SOURCES.txt' Copying GroopM.egg-info to /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/GroopM-0.3.4-py2.7.egg-info running install_scripts copying build/scripts-2.7/groopm -> /construction/biology/groopm/stage/usr/local/bin changing mode of /construction/biology/groopm/stage/usr/local/bin/groopm to 755 writing list of installed files to '/construction/biology/groopm/.PLIST.pymodtmp' ====> 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 00:00:02 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for GroopM-0.3.4_2 file sizes/checksums [54]: 0% file sizes/checksums [54]: 100% packing files [54]: 0% packing files [54]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:01:20