------------------------------------------------------------------------------- -- 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. 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Installing /packages/All/etc_os-release-0.1_2.tgz Installing /packages/All/qtchooser-66.tgz Message from qtchooser-66: qtchooser is a wrapper that allows selecting whether Qt4 or Qt5 binaries for qmake, moc and other tools will be run when invoking the binaries in $PATH. By default, the Qt5 versions are run. It is possible to change the behavior by setting the QT_SELECT environment variable to "qt4". See qtchooser(1) for more information. Installing /packages/All/qt5-core-5.12.2_2.tgz Installing /packages/All/libICE-1.0.9_3,1.tgz Installing /packages/All/libSM-1.2.3,1.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/dbus-1.12.12.tgz ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. 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. 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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/graphite2-1.3.13_1.tgz Installing /packages/All/png-1.6.37.tgz Installing /packages/All/wayland-1.16.0.tgz Installing /packages/All/pciids-20190725.tgz Installing /packages/All/libpciaccess-0.16.tgz Installing /packages/All/libdrm-2.4.99.tgz Installing /packages/All/libelf-0.8.13_3.tgz Installing /packages/All/libXfixes-5.0.3_2.tgz Installing /packages/All/libXdamage-1.1.5.tgz Installing /packages/All/libXext-1.3.4,1.tgz Installing /packages/All/libXrender-0.9.10_2.tgz Installing /packages/All/libXrandr-1.5.2.tgz Installing /packages/All/libxshmfence-1.3.tgz Installing /packages/All/libXxf86vm-1.1.4_3.tgz Installing /packages/All/mesa-libs-18.3.2_1.tgz Installing /packages/All/pixman-0.38.4.tgz Installing /packages/All/cairo-1.16.0,2.tgz Installing /packages/All/harfbuzz-2.5.3_1.tgz Installing /packages/All/xcb-util-0.4.0_2,1.tgz Installing /packages/All/xcb-util-image-0.4.0_1.tgz Installing /packages/All/xcb-util-keysyms-0.4.0_1.tgz Installing /packages/All/xcb-util-renderutil-0.3.9_1.tgz Installing /packages/All/xcb-util-wm-0.4.1_3.tgz Installing /packages/All/xkeyboard-config-2.27.tgz Installing /packages/All/libxkbcommon-0.8.4.tgz Installing /packages/All/jpeg-turbo-2.0.2.tgz Installing /packages/All/qt5-dbus-5.12.2_1.tgz Installing /packages/All/qt5-network-5.12.2_2.tgz Installing /packages/All/hicolor-icon-theme-0.17.tgz Installing /packages/All/xprop-1.2.4.tgz Installing /packages/All/libXt-1.2.0,1.tgz Installing /packages/All/libXmu-1.1.3,1.tgz Installing /packages/All/libXfontcache-1.0.5_5.tgz Installing /packages/All/xset-1.2.4_2.tgz Installing /packages/All/xdg-utils-1.1.3_1.tgz Installing /packages/All/libXi-1.7.10,1.tgz Installing /packages/All/qt5-gui-5.12.2_1.tgz Installing /packages/All/qt5-widgets-5.12.2_1.tgz Installing /packages/All/molequeue-0.9.0_3.tgz Installing /packages/All/spglib-1.12.2.tgz Installing /packages/All/libGLU-9.0.0_3.tgz Installing /packages/All/glew-2.1.0.tgz Installing /packages/All/qt5-concurrent-5.12.2_1.tgz Installing /packages/All/avogadrolibs-1.92.1_1.tgz SUCCEEDED 00:00:19 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-avogadrolibs-1.91.0.107_4 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-avogadrolibs-1.91.0.107_4 for building => SHA256 Checksum OK for OpenChemistry-avogadrolibs-1.91.0-107-g60c69b0_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py36-avogadrolibs-1.91.0.107_4 for building ===> Extracting for py36-avogadrolibs-1.91.0.107_4 => SHA256 Checksum OK for OpenChemistry-avogadrolibs-1.91.0-107-g60c69b0_GH0.tar.gz. Extracted Memory Use: 14.50M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- x===> Patching for py36-avogadrolibs-1.91.0.107_4 ===> Applying ports patches for py36-avogadrolibs-1.91.0.107_4 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 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components: Interpreter -- Found PythonLibs: /usr/local/lib/libpython3.6m.so (found suitable version "3.6.9", minimum required is "3") -- Found PythonInterp: /usr/local/bin/python3.6 (found suitable version "3.6.9", minimum required is "3") -- Found PythonLibs: /usr/local/lib/libpython3.6m.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- LTO enabled -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_EXE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /construction/science/py-avogadrolibs/.build SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- x===> Building for py36-avogadrolibs-1.91.0.107_4 /usr/local/bin/cmake -S/construction/science/py-avogadrolibs/avogadrolibs-1.91.0-107-g60c69b0/python -B/construction/science/py-avogadrolibs/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/science/py-avogadrolibs/.build/CMakeFiles /construction/science/py-avogadrolibs/.build/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/avogadroiopython.dir/all --- --- CMakeFiles/avogadrocorepython.dir/all --- --- CMakeFiles/avogadroiopython.dir/all --- /usr/bin/make -f CMakeFiles/avogadroiopython.dir/build.make CMakeFiles/avogadroiopython.dir/depend --- CMakeFiles/avogadrocorepython.dir/all --- /usr/bin/make -f CMakeFiles/avogadrocorepython.dir/build.make CMakeFiles/avogadrocorepython.dir/depend --- CMakeFiles/avogadrocorepython.dir/depend --- cd /construction/science/py-avogadrolibs/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/py-avogadrolibs/avogadrolibs-1.91.0-107-g60c69b0/python /construction/science/py-avogadrolibs/avogadrolibs-1.91.0-107-g60c69b0/python /construction/science/py-avogadrolibs/.build /construction/science/py-avogadrolibs/.build /construction/science/py-avogadrolibs/.build/CMakeFiles/avogadrocorepython.dir/DependInfo.cmake --- CMakeFiles/avogadroiopython.dir/all --- --- CMakeFiles/avogadroiopython.dir/depend --- cd /construction/science/py-avogadrolibs/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/py-avogadrolibs/avogadrolibs-1.91.0-107-g60c69b0/python /construction/science/py-avogadrolibs/avogadrolibs-1.91.0-107-g60c69b0/python /construction/science/py-avogadrolibs/.build /construction/science/py-avogadrolibs/.build /construction/science/py-avogadrolibs/.build/CMakeFiles/avogadroiopython.dir/DependInfo.cmake --- CMakeFiles/avogadrocorepython.dir/all --- Scanning dependencies of target avogadrocorepython /usr/bin/make -f 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CMakeFiles/avogadroiopython.dir/io.cpp.o /usr/bin/c++ -Davogadroiopython_EXPORTS -isystem /avogadro/core -isystem /avogadro/io -isystem /avogadro/quantumio -isystem /usr/local/include/python3.6m -isystem /usr/local/include/eigen3 -isystem /usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -fvisibility=hidden -std=c++11 -flto -fno-fat-lto-objects -fvisibility=hidden -o CMakeFiles/avogadroiopython.dir/io.cpp.o -c /construction/science/py-avogadrolibs/avogadrolibs-1.91.0-107-g60c69b0/python/io.cpp --- lib/avogadro/io.so --- [ 50%] Linking CXX shared module lib/avogadro/io.so /usr/local/bin/cmake -E cmake_link_script CMakeFiles/avogadroiopython.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -shared -o lib/avogadro/io.so CMakeFiles/avogadroiopython.dir/io.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib -flto -lAvogadroIO -lAvogadroQuantumIO --- CMakeFiles/avogadrocorepython.dir/all --- --- lib/avogadro/core.so --- [ 66%] Linking CXX shared module lib/avogadro/core.so /usr/local/bin/cmake -E cmake_link_script CMakeFiles/avogadrocorepython.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -shared -o lib/avogadro/core.so CMakeFiles/avogadrocorepython.dir/core.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib -flto -lAvogadroCore --- CMakeFiles/avogadroiopython.dir/all --- /usr/bin/strip /construction/science/py-avogadrolibs/.build/lib/avogadro/io.so [ 83%] Built target avogadroiopython --- CMakeFiles/avogadrocorepython.dir/all --- /usr/bin/strip /construction/science/py-avogadrolibs/.build/lib/avogadro/core.so [100%] Built target avogadrocorepython /usr/local/bin/cmake -E cmake_progress_start /construction/science/py-avogadrolibs/.build/CMakeFiles 0 SUCCEEDED 00:00:27 ------------------------------------------------------------------------------- -- Phase: run-depends 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/construction/science/py-avogadrolibs/avogadrolibs-1.91.0-107-g60c69b0/python /construction/science/py-avogadrolibs/avogadrolibs-1.91.0-107-g60c69b0/python /construction/science/py-avogadrolibs/.build /construction/science/py-avogadrolibs/.build /construction/science/py-avogadrolibs/.build/CMakeFiles/avogadroiopython.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/avogadroiopython.dir/build.make CMakeFiles/avogadroiopython.dir/build [ 50%] Built target avogadroiopython /usr/bin/make -f CMakeFiles/avogadrocorepython.dir/build.make CMakeFiles/avogadrocorepython.dir/depend cd /construction/science/py-avogadrolibs/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/py-avogadrolibs/avogadrolibs-1.91.0-107-g60c69b0/python /construction/science/py-avogadrolibs/avogadrolibs-1.91.0-107-g60c69b0/python /construction/science/py-avogadrolibs/.build /construction/science/py-avogadrolibs/.build 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CMakeFiles/avogadrocorepython.dir/preinstall Linking CXX shared module CMakeFiles/CMakeRelink.dir/core.so /usr/local/bin/cmake -E cmake_link_script CMakeFiles/avogadrocorepython.dir/relink.txt --verbose=1 /usr/bin/c++ -fPIC -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -shared -o CMakeFiles/CMakeRelink.dir/core.so CMakeFiles/avogadrocorepython.dir/core.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,"\$ORIGIN:/usr/local/lib" -flto -lAvogadroCore Installing the project stripped... /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /construction/science/py-avogadrolibs/stage/usr/local/lib/python3.6/site-packages/avogadro/core.so -- Installing: /construction/science/py-avogadrolibs/stage/usr/local/lib/python3.6/site-packages/avogadro/io.so -- Installing: /construction/science/py-avogadrolibs/stage/usr/local/lib/python3.6/site-packages/avogadro/__init__.py ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.6/site-packages/avogadro/core.so is linked to /usr/local/lib/libsymspg.so.0 from science/spglib but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libsymspg.so:science/spglib Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:22 ------------------------------------------------------------------------------- -- 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 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- x===> Building 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