------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/expat-2.2.6_1.tgz Installing /packages/All/indexinfo-0.3.1.tgz Installing /packages/All/libffi-3.2.1_3.tgz Installing /packages/All/ncurses-6.1.20190525.tgz Installing /packages/All/readline-8.0.0.tgz Installing /packages/All/gettext-runtime-0.20.1.tgz Installing /packages/All/openssl-1.0.2s,1.tgz Message from openssl-1.0.2s,1: Edit /usr/local/openssl/openssl.cnf to fit your needs. Installing /packages/All/python36-3.6.9.tgz 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 =========================================================================== Installing /packages/All/py36-setuptools-41.0.1.tgz Installing /packages/All/libxml2-2.9.9.tgz Installing /packages/All/libgpg-error-1.36.tgz Installing /packages/All/libgcrypt-1.8.4_1.tgz Installing /packages/All/libxslt-1.1.33.tgz Installing /packages/All/py36-lxml-4.3.4_1.tgz Installing /packages/All/freetype2-2.10.1.tgz Message from freetype2-2.10.1: 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. 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.tgz Installing /packages/All/fontconfig-2.12.6,1.tgz 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 /packages/All/tcl86-8.6.9_1.tgz Installing /packages/All/metis-5.1.0_8.tgz Message from metis-5.1.0_8: ===> 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 Installing /packages/All/gmp-6.1.2_1.tgz Installing /packages/All/mpfr-4.0.2.tgz Installing /packages/All/mpc-1.1.0_2.tgz Installing /packages/All/binutils-2.32_1,1.tgz Installing /packages/All/gcc8-8.3.0_3.tgz Message from gcc8-8.3.0_3: 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/blas-3.5.0_6.tgz Installing /packages/All/lapack-3.5.0_8.tgz Installing /packages/All/openblas-0.2.20_10,1.tgz Installing /packages/All/suitesparse-5.2.0_4.tgz Installing /packages/All/py36-numpy-1.16.4_1,1.tgz Installing /packages/All/py36-six-1.12.0.tgz Installing /packages/All/py36-cycler-0.10.0.tgz Installing /packages/All/py36-dateutil-2.8.0.tgz Installing /packages/All/py36-pytz-2019.1,1.tgz Installing /packages/All/py36-pyparsing-2.4.1.1.tgz Installing /packages/All/py36-tornado-5.1.1.tgz Installing /packages/All/py36-kiwisolver-1.1.0.tgz Installing /packages/All/libXau-1.0.9.tgz Installing /packages/All/xorgproto-2019.1.tgz Installing /packages/All/libXdmcp-1.1.3.tgz Installing /packages/All/libpthread-stubs-0.4.tgz Installing /packages/All/libxcb-1.13.1.tgz Installing /packages/All/libX11-1.6.8,1.tgz Installing /packages/All/libXext-1.3.4,1.tgz Installing /packages/All/libXrender-0.9.10_2.tgz Installing /packages/All/libXft-2.3.2_3.tgz Installing /packages/All/libXScrnSaver-1.2.3_2.tgz Installing /packages/All/tk86-8.6.9_1.tgz Installing /packages/All/py36-tkinter-3.6.9_6.tgz Installing /packages/All/py36-matplotlib-2.2.4_1.tgz Installing /packages/All/sqlite3-3.29.0.tgz Installing /packages/All/py36-sqlite3-3.6.9_7.tgz Installing /packages/All/py36-bottleneck-1.2.1_5.tgz Installing /packages/All/py36-numexpr-2.6.9_1.tgz Installing /packages/All/py36-pandas-0.24.2_1.tgz Message from py36-pandas-0.24.2_1: === Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. === Installing /packages/All/py36-sqlalchemy13-1.3.6.tgz SUCCEEDED 00:00:21 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-pyteomics-4.1.2_1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-pyteomics-4.1.2_1 for building => SHA256 Checksum OK for pyteomics-4.1.2.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-pyteomics-4.1.2_1 for building ===> Extracting for py36-pyteomics-4.1.2_1 => SHA256 Checksum OK for pyteomics-4.1.2.tar.gz. Extracted Memory Use: 1.12M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- x===> Patching for py36-pyteomics-4.1.2_1 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- x===> Configuring for py36-pyteomics-4.1.2_1 running config SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- x===> Building for py36-pyteomics-4.1.2_1 running build running build_py creating build creating build/lib creating build/lib/pyteomics copying pyteomics/achrom.py -> build/lib/pyteomics copying pyteomics/mzml.py -> build/lib/pyteomics copying pyteomics/pylab_aux.py -> build/lib/pyteomics copying pyteomics/mzid.py -> build/lib/pyteomics copying pyteomics/mgf.py -> build/lib/pyteomics copying pyteomics/peff.py -> build/lib/pyteomics copying pyteomics/mztab.py -> build/lib/pyteomics copying pyteomics/ms1.py -> build/lib/pyteomics copying pyteomics/tandem.py -> build/lib/pyteomics copying pyteomics/__init__.py -> build/lib/pyteomics copying pyteomics/parser.py -> build/lib/pyteomics copying pyteomics/fasta.py -> build/lib/pyteomics copying pyteomics/mzxml.py -> build/lib/pyteomics copying pyteomics/xml.py -> build/lib/pyteomics copying pyteomics/pepxml.py -> build/lib/pyteomics copying pyteomics/ms2.py -> build/lib/pyteomics copying pyteomics/protxml.py -> build/lib/pyteomics copying pyteomics/electrochem.py -> build/lib/pyteomics copying pyteomics/_schema_defaults.py -> build/lib/pyteomics copying pyteomics/traml.py -> build/lib/pyteomics creating build/lib/pyteomics/mass copying pyteomics/mass/mass.py -> build/lib/pyteomics/mass copying pyteomics/mass/unimod.py -> build/lib/pyteomics/mass copying pyteomics/mass/__init__.py -> build/lib/pyteomics/mass creating build/lib/pyteomics/openms copying pyteomics/openms/featurexml.py -> build/lib/pyteomics/openms copying pyteomics/openms/trafoxml.py -> build/lib/pyteomics/openms copying pyteomics/openms/__init__.py -> build/lib/pyteomics/openms creating build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/patch.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/constants.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/utils.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/target_decoy.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/structures.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/__init__.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/math.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/file_helpers.py -> build/lib/pyteomics/auxiliary SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- x===> Staging for py36-pyteomics-4.1.2_1 ===> Generating temporary packing list running install running build running build_py running install_lib copying pyteomics/_schema_defaults.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/mgf.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/ms2.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/ms1.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/parser.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/protxml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/mzid.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics Skipping installation of /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/__init__.py (namespace package) copying pyteomics/achrom.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/pylab_aux.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/pepxml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/xml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/mzml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/fasta.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/electrochem.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/peff.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/mztab.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/traml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/tandem.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/mzxml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics copying pyteomics/mass/__init__.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/mass copying pyteomics/mass/unimod.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/mass copying pyteomics/mass/mass.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/mass copying pyteomics/openms/__init__.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/openms copying pyteomics/openms/trafoxml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/openms copying pyteomics/openms/featurexml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/openms copying pyteomics/auxiliary/file_helpers.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/patch.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/__init__.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/utils.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/constants.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/math.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/target_decoy.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/structures.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/_schema_defaults.py to _schema_defaults.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/mgf.py to mgf.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/ms2.py to ms2.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/ms1.py to ms1.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/parser.py to parser.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/protxml.py to protxml.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/mzid.py to mzid.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/achrom.py to achrom.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/pylab_aux.py to pylab_aux.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/pepxml.py to pepxml.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/xml.py to xml.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/mzml.py to mzml.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/fasta.py to fasta.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/electrochem.py to electrochem.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/peff.py to peff.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/mztab.py to mztab.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/traml.py to traml.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/tandem.py to tandem.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/mzxml.py to mzxml.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/mass/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/mass/unimod.py to unimod.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/mass/mass.py to mass.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/openms/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/openms/trafoxml.py to trafoxml.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/openms/featurexml.py to featurexml.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary/file_helpers.py to file_helpers.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary/patch.py to patch.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary/__init__.py to __init__.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary/utils.py to utils.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary/constants.py to constants.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary/math.py to math.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary/target_decoy.py to target_decoy.cpython-36.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics/auxiliary/structures.py to structures.cpython-36.pyc writing byte-compilation script '/tmp/tmps9712zxm.py' /usr/local/bin/python3.6 /tmp/tmps9712zxm.py removing /tmp/tmps9712zxm.py running install_egg_info running egg_info writing pyteomics.egg-info/PKG-INFO writing dependency_links to pyteomics.egg-info/dependency_links.txt writing namespace_packages to pyteomics.egg-info/namespace_packages.txt writing requirements to pyteomics.egg-info/requires.txt writing top-level names to pyteomics.egg-info/top_level.txt reading manifest file 'pyteomics.egg-info/SOURCES.txt' writing manifest file 'pyteomics.egg-info/SOURCES.txt' Copying pyteomics.egg-info to /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics-4.1.2-py3.6.egg-info Installing /construction/science/py-pyteomics/stage/usr/local/lib/python3.6/site-packages/pyteomics-4.1.2-py3.6-nspkg.pth running install_scripts writing list of installed files to '/construction/science/py-pyteomics/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX ====> 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 ------------------------------------------------------------------------------- x====> 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 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- x===> Building package for py36-pyteomics-4.1.2_1 file sizes/checksums [107]: 0% file sizes/checksums [107]: 93% file sizes/checksums [107]: 100% packing files [107]: 0% packing files [107]: 93% packing files [107]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:00:34