build.log

kalzium-20.04.0:20200427-150145.log (text/x-log), 31.55 KB, created by Thomas Posch on 2020-04-27 15:43:42 UTC

 * Package:    kde-apps/kalzium-20.04.0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 editor elibc_glibc handbook kernel_linux solver userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking kalzium-20.04.0.tar.xz to /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work
>>> Source unpacked in /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work
>>> Preparing source in /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0 ...
 * Working in BUILD_DIR: "/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build"
>>> Source prepared.
>>> Configuring source in /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0 ...
 * Working in BUILD_DIR: "/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build"
cmake -C /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DKDE_INSTALL_USE_QT_SYS_PATHS=ON -DKDE_INSTALL_DOCBUNDLEDIR=/usr/share/help -DCMAKE_DISABLE_FIND_PACKAGE_Eigen3=OFF -DCMAKE_DISABLE_FIND_PACKAGE_AvogadroLibs=OFF -DCMAKE_DISABLE_FIND_PACKAGE_OpenBabel2=OFF -DCMAKE_DISABLE_FIND_PACKAGE_OCaml=OFF -DCMAKE_DISABLE_FIND_PACKAGE_Libfacile=OFF -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build/gentoo_toolchain.cmake  /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0
loading initial cache file /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build/gentoo_common_config.cmake
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for __GLIBC__
-- Looking for __GLIBC__ - found
-- Performing Test _OFFT_IS_64BIT
-- Performing Test _OFFT_IS_64BIT - Success
-- Performing Test HAVE_DATE_TIME
-- Performing Test HAVE_DATE_TIME - Success
-- Could not set up the appstream test. appstreamcli is missing.
-- Found Gettext: /usr/bin/msgmerge (found version "0.20.1") 
-- Found PythonInterp: /usr/bin/python (found version "3.6.10") 
-- Found PkgConfig: x86_64-pc-linux-gnu-pkg-config (found version "0.29.2") 
-- Checking for module 'openbabel-2.0>=2.2.0'
--   Found openbabel-2.0, version 2.4.1
-- Found OpenBabel 2.2 or later: /usr/lib64/libopenbabel.so
-- Found OpenBabel2 executable: /usr/bin/babel
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
-- Found OCaml: /usr/bin/ocamlc
-- Found Libfacile: /usr/lib64/ocaml/facile  
-- Checking for module 'chemical-mime-data'
--   Found chemical-mime-data, version 0.1.94
-- Looking for include file ieeefp.h
-- Looking for include file ieeefp.h - not found
-- Found KF5Archive: /usr/lib64/cmake/KF5Archive/KF5ArchiveConfig.cmake (found version "5.69.0") 
-- Found KF5Config: /usr/lib64/cmake/KF5Config/KF5ConfigConfig.cmake (found version "5.69.0") 
-- Found KF5CoreAddons: /usr/lib64/cmake/KF5CoreAddons/KF5CoreAddonsConfig.cmake (found version "5.69.0") 
-- Found KF5DocTools: /usr/lib64/cmake/KF5DocTools/KF5DocToolsConfig.cmake (found version "5.69.0") 
-- Found KF5I18n: /usr/lib64/cmake/KF5I18n/KF5I18nConfig.cmake (found version "5.69.0") 
-- Found KF5Parts: /usr/lib64/cmake/KF5Parts/KF5PartsConfig.cmake (found version "5.69.0") 
-- Found KF5Plotting: /usr/lib64/cmake/KF5Plotting/KF5PlottingConfig.cmake (found version "5.69.0") 
-- Found KF5Solid: /usr/lib64/cmake/KF5Solid/KF5SolidConfig.cmake (found version "5.69.0") 
-- Found KF5UnitConversion: /usr/lib64/cmake/KF5UnitConversion/KF5UnitConversionConfig.cmake (found version "5.69.0") 
-- Found KF5WidgetsAddons: /usr/lib64/cmake/KF5WidgetsAddons/KF5WidgetsAddonsConfig.cmake (found version "5.69.0") 
-- Found KF5: success (found suitable version "5.69.0", minimum required is "5.42.0") found components: Archive Config CoreAddons DocTools I18n Parts Plotting Solid UnitConversion WidgetsAddons 
-- Kalzium molecular editor enabled
-- The following OPTIONAL packages have been found:

 * OpenBabel2
 * AvogadroLibs
 * Eigen3
 * OCaml
 * Libfacile
 * KF5Bookmarks (required version >= 5.69.0)
 * KF5Completion (required version >= 5.69.0)
 * KF5ItemViews (required version >= 5.69.0)
 * KF5JobWidgets (required version >= 5.69.0)
 * KF5WindowSystem (required version >= 5.69.0)
 * KF5Sonnet (required version >= 5.69.0)
 * KF5TextWidgets (required version >= 5.69.0)

-- The following REQUIRED packages have been found:

 * ECM (required version >= 5.42.0)
 * PythonInterp
 * PkgConfig
 * Qt5Gui
 * Qt5Script
 * Qt5Svg
 * Qt5 (required version >= 5.9.0)
 * KF5Archive (required version >= 5.42.0)
 * KF5DocTools (required version >= 5.42.0)
 * Gettext
 * KF5I18n (required version >= 5.69.0)
 * KF5Parts (required version >= 5.42.0)
 * KF5Plotting (required version >= 5.42.0)
 * KF5Solid (required version >= 5.42.0)
 * KF5UnitConversion (required version >= 5.42.0)
 * KF5 (required version >= 5.42.0)
 * Qt5OpenGL (required version >= 5.9.0)
 * KF5Auth (required version >= 5.69.0)
 * KF5Codecs (required version >= 5.69.0)
 * Qt5Widgets (required version >= 5.12.0)
 * KF5WidgetsAddons (required version >= 5.69.0)
 * KF5ConfigWidgets (required version >= 5.69.0)
 * KF5XmlGui (required version >= 5.69.0)
 * Qt5Xml (required version >= 5.12.0)
 * KF5Config (required version >= 5.69.0)
 * KF5CoreAddons (required version >= 5.69.0)
 * KF5Service (required version >= 5.69.0)
 * Qt5Core (required version >= 5.12.0)
 * KF5NewStuff

-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -falign-functions=32 -finline-functions -fomit-frame-pointer -march=native -O2 -pipe -fno-common -Wall -Wextra -Wcast-align -Wchar-subscripts -Wformat-security -Wno-long-long -Wpointer-arith -Wundef -Wmissing-format-attribute -Wwrite-strings -Werror=implicit-function-declaration
C++             -falign-functions=32 -finline-functions -fomit-frame-pointer -march=native -O2 -pipe -fno-operator-names -fno-exceptions -Wall -Wextra -Wcast-align -Wchar-subscripts -Wformat-security -Wno-long-long -Wpointer-arith -Wundef -Wnon-virtual-dtor -Woverloaded-virtual -Werror=return-type -Wvla -Wdate-time -Wsuggest-override -Wlogical-op -fdiagnostics-color=always
Linker flags:
Executable      -Wl,--enable-new-dtags -Wl,-O1 -Wl,--as-needed
Module          -Wl,--no-undefined -Wl,--enable-new-dtags -Wl,-O1 -Wl,--as-needed
Shared          -Wl,--no-undefined -Wl,--enable-new-dtags -Wl,-O1 -Wl,--as-needed

-- Configuring done
-- Generating done
-- Build files have been written to: /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build
>>> Source configured.
>>> Compiling source in /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0 ...
 * Working in BUILD_DIR: "/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build"
ninja -v -j20 -l26
[1/119] cd /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build && /usr/bin/cmake -DPYTHON_EXECUTABLE=/usr/bin/python -D_ki18n_pmap_compile_script=/usr/lib64/cmake/KF5I18n/ts-pmap-compile.py -DCOPY_TO=/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build/locale -DPO_DIR=/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/po -P /usr/lib64/cmake/KF5I18n/build-tsfiles.cmake
[2/119] cd /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build/libscience && /usr/bin/cmake -E cmake_autogen /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build/libscience/CMakeFiles/science_autogen.dir/AutogenInfo.json Gentoo
[3/119] /usr/bin/x86_64-pc-linux-gnu-g++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_NO_URL_CAST_FROM_STRING -DQT_WIDGETS_LIB -DQT_XML_LIB -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -Dscience_EXPORTS -Ilibscience -I/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/libscience -Ilibscience/science_autogen/include -isystem /usr/include/qt5 -isystem /usr/include/qt5/QtXml -isystem /usr/include/qt5/QtCore -isystem /usr/lib64/qt5/mkspecs/linux-g++ -isystem /usr/include/KF5/KUnitConversion -isystem /usr/include/KF5 -isystem /usr/include/KF5/KWidgetsAddons -isystem /usr/include/qt5/QtWidgets -isystem /usr/include/qt5/QtGui -isystem /usr/include/KF5/KI18n  -DQT_NO_DEBUG -falign-functions=32 -finline-functions -fomit-frame-pointer -march=native -O2 -pipe -fno-operator-names -fno-exceptions -Wall -Wextra -Wcast-align -Wchar-subscripts -Wformat-security -Wno-long-long -Wpointer-arith -Wundef -Wnon-virtual-dtor -Woverloaded-virtual -Werror=return-type -Wvla -Wdate-time -Wsuggest-override -Wlogical-op -fdiagnostics-color=always -fPIC -fvisibility=hidden -fvisibility-inlines-hidden   -fPIC -std=gnu++11 -MD -MT libscience/CMakeFiles/science.dir/science_autogen/mocs_compilation.cpp.o -MF libscience/CMakeFiles/science.dir/science_autogen/mocs_compilation.cpp.o.d -o libscience/CMakeFiles/science.dir/science_autogen/mocs_compilation.cpp.o -c libscience/science_autogen/mocs_compilation.cpp
[4/119] cd /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build && /usr/bin/cmake -DGETTEXT_MSGFMT_EXECUTABLE=/usr/bin/msgfmt -DCOPY_TO=/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build/locale -DPO_DIR=/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/po -P /usr/lib64/cmake/KF5I18n/build-pofiles.cmake
[5/119] cd /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build/doc && /usr/bin/meinproc5 --stylesheet /usr/share/kf5/kdoctools/customization/kde-include-man.xsl --check /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/doc/man-kalzium.1.docbook
Note: Writing kalzium.1
[6/119] cd /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build/compoundviewer && /usr/bin/cmake -E cmake_autogen /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build/compoundviewer/CMakeFiles/compoundviewer_autogen.dir/AutogenInfo.json Gentoo
[7/119] cd /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/doc && /usr/bin/meinproc5 --check --cache /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build/doc//index.cache.bz2 index.docbook
[8/119] /usr/bin/x86_64-pc-linux-gnu-g++ -DKCOREADDONS_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_NO_URL_CAST_FROM_STRING -DQT_OPENGL_LIB -DQT_WIDGETS_LIB -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -Dcompoundviewer_EXPORTS -Icompoundviewer -I/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/compoundviewer -Icompoundviewer/compoundviewer_autogen/include -Icompoundviewer/.. -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -isystem /usr/include/KF5/KI18n -isystem /usr/include/KF5 -isystem /usr/include/qt5 -isystem /usr/include/qt5/QtCore -isystem /usr/lib64/qt5/mkspecs/linux-g++ -isystem /usr/include/KF5/KWidgetsAddons -isystem /usr/include/qt5/QtWidgets -isystem /usr/include/qt5/QtGui -isystem /usr/include/KF5/KCoreAddons -isystem /usr/include/qt5/QtOpenGL  -DQT_NO_DEBUG -falign-functions=32 -finline-functions -fomit-frame-pointer -march=native -O2 -pipe -fno-operator-names -fno-exceptions -Wall -Wextra -Wcast-align -Wchar-subscripts -Wformat-security -Wno-long-long -Wpointer-arith -Wundef -Wnon-virtual-dtor -Woverloaded-virtual -Werror=return-type -Wvla -Wdate-time -Wsuggest-override -Wlogical-op -fdiagnostics-color=always -fPIC -fvisibility=hidden -fvisibility-inlines-hidden   -fPIC -std=gnu++14 -MD -MT compoundviewer/CMakeFiles/compoundviewer.dir/iowrapper.cpp.o -MF compoundviewer/CMakeFiles/compoundviewer.dir/iowrapper.cpp.o.d -o compoundviewer/CMakeFiles/compoundviewer.dir/iowrapper.cpp.o -c /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/compoundviewer/iowrapper.cpp
FAILED: compoundviewer/CMakeFiles/compoundviewer.dir/iowrapper.cpp.o 
/usr/bin/x86_64-pc-linux-gnu-g++ -DKCOREADDONS_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_NO_URL_CAST_FROM_STRING -DQT_OPENGL_LIB -DQT_WIDGETS_LIB -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -Dcompoundviewer_EXPORTS -Icompoundviewer -I/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/compoundviewer -Icompoundviewer/compoundviewer_autogen/include -Icompoundviewer/.. -I/usr/include/eigen3 -I/usr/include/openbabel-2.0 -isystem /usr/include/KF5/KI18n -isystem /usr/include/KF5 -isystem /usr/include/qt5 -isystem /usr/include/qt5/QtCore -isystem /usr/lib64/qt5/mkspecs/linux-g++ -isystem /usr/include/KF5/KWidgetsAddons -isystem /usr/include/qt5/QtWidgets -isystem /usr/include/qt5/QtGui -isystem /usr/include/KF5/KCoreAddons -isystem /usr/include/qt5/QtOpenGL  -DQT_NO_DEBUG -falign-functions=32 -finline-functions -fomit-frame-pointer -march=native -O2 -pipe -fno-operator-names -fno-exceptions -Wall -Wextra -Wcast-align -Wchar-subscripts -Wformat-security -Wno-long-long -Wpointer-arith -Wundef -Wnon-virtual-dtor -Woverloaded-virtual -Werror=return-type -Wvla -Wdate-time -Wsuggest-override -Wlogical-op -fdiagnostics-color=always -fPIC -fvisibility=hidden -fvisibility-inlines-hidden   -fPIC -std=gnu++14 -MD -MT compoundviewer/CMakeFiles/compoundviewer.dir/iowrapper.cpp.o -MF compoundviewer/CMakeFiles/compoundviewer.dir/iowrapper.cpp.o.d -o compoundviewer/CMakeFiles/compoundviewer.dir/iowrapper.cpp.o -c /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/compoundviewer/iowrapper.cpp
[01m[K/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/compoundviewer/iowrapper.cpp:23:10:[m[K [01;31m[Kfatal error: [m[Kavogadro/io/pdbformat.h: No such file or directory
   23 | #include [01;31m[K<avogadro/io/pdbformat.h>[m[K
      |          [01;31m[K^~~~~~~~~~~~~~~~~~~~~~~~~[m[K
compilation terminated.
[9/119] /usr/bin/x86_64-pc-linux-gnu-g++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_NO_URL_CAST_FROM_STRING -DQT_WIDGETS_LIB -DQT_XML_LIB -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -Dscience_EXPORTS -Ilibscience -I/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/libscience -Ilibscience/science_autogen/include -isystem /usr/include/qt5 -isystem /usr/include/qt5/QtXml -isystem /usr/include/qt5/QtCore -isystem /usr/lib64/qt5/mkspecs/linux-g++ -isystem /usr/include/KF5/KUnitConversion -isystem /usr/include/KF5 -isystem /usr/include/KF5/KWidgetsAddons -isystem /usr/include/qt5/QtWidgets -isystem /usr/include/qt5/QtGui -isystem /usr/include/KF5/KI18n  -DQT_NO_DEBUG -falign-functions=32 -finline-functions -fomit-frame-pointer -march=native -O2 -pipe -fno-operator-names -fno-exceptions -Wall -Wextra -Wcast-align -Wchar-subscripts -Wformat-security -Wno-long-long -Wpointer-arith -Wundef -Wnon-virtual-dtor -Woverloaded-virtual -Werror=return-type -Wvla -Wdate-time -Wsuggest-override -Wlogical-op -fdiagnostics-color=always -fPIC -fvisibility=hidden -fvisibility-inlines-hidden   -fPIC -std=gnu++11 -MD -MT libscience/CMakeFiles/science.dir/chemicaldataobject.cpp.o -MF libscience/CMakeFiles/science.dir/chemicaldataobject.cpp.o.d -o libscience/CMakeFiles/science.dir/chemicaldataobject.cpp.o -c /mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0/libscience/chemicaldataobject.cpp
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ninja: build stopped: subcommand failed.
 * ERROR: kde-apps/kalzium-20.04.0::gentoo failed (compile phase):
 *   ninja -v -j20 -l26 failed
 * 
 * Call stack:
 *     ebuild.sh, line  125:  Called src_compile
 *   environment, line 2461:  Called cmake_src_compile
 *   environment, line  959:  Called cmake_build
 *   environment, line  938:  Called eninja
 *   environment, line 1567:  Called die
 * The specific snippet of code:
 *       "$@" || die "${nonfatal_args[@]}" "${*} failed"
 * 
 * If you need support, post the output of `emerge --info '=kde-apps/kalzium-20.04.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=kde-apps/kalzium-20.04.0::gentoo'`.
 * The complete build log is located at '/var/log/portage/build/kde-apps/kalzium-20.04.0:20200427-150145.log'.
 * For convenience, a symlink to the build log is located at '/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/temp/build.log'.
 * The ebuild environment file is located at '/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/temp/environment'.
 * Working directory: '/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0_build'
 * S: '/mnt/tmpfs/portage/kde-apps/kalzium-20.04.0/work/kalzium-20.04.0'