sci-libs:avogadrolibs-1.93.0:20210826-170820.log

sci-libs:avogadrolibs-1.93.0:20210826-170820.log (text/plain), 49.09 KB, created by Toralf Förster on 2021-08-26 17:18:41 UTC

 * Package:    sci-libs/avogadrolibs-1.93.0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc hdf5 kernel_linux qt5 userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking avogadrolibs-1.93.0.tar.gz to /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work
>>> Source unpacked in /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work
>>> Preparing source in /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 ...
 * Applying avogadrolibs-1.93.0-fix_AvogadroLibsConfig.patch ...
 [ ok ]
 * Applying avogadrolibs-1.91.0_pre20180406-bundled-genxrdpattern.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build"
cmake -C /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/avogadrolibs-1.93.0 -DUSE_PROTOCALL=OFF -DBUILD_GPL_PLUGINS=ON -DUSE_MOLEQUEUE=ON -DUSE_MMTF=OFF -DUSE_LIBMSYM=OFF -DUSE_SPGLIB=OFF -DUSE_PYTHON=OFF -DUSE_LIBARCHIVE=no -DBUILD_DOCUMENTATION=no -DUSE_HDF5=yes -DENABLE_TRANSLATIONS=yes -DUSE_OPENGL=yes -DUSE_QT=yes -DBUILD_STATIC_PLUGINS=ON -DENABLE_TESTING=no -DUSE_VTK=no -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/gentoo_toolchain.cmake  /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0
loading initial cache file /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/gentoo_common_config.cmake
-- The C compiler identification is GNU 11.2.0
-- The CXX compiler identification is GNU 11.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_GCC_ERROR_RETURN_TYPE
-- Performing Test HAVE_GCC_ERROR_RETURN_TYPE - Success
-- Found Git: /usr/bin/git (found version "2.33.0") 
-- Could not use git to determine source version, using version 1.93.0
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Found HDF5: hdf5-shared (found version "1.12.1") found components: C 
CMake Warning (dev) at /usr/share/cmake/Modules/FindOpenGL.cmake:315 (message):
  Policy CMP0072 is not set: FindOpenGL prefers GLVND by default when
  available.  Run "cmake --help-policy CMP0072" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  FindOpenGL found both a legacy GL library:

    OPENGL_gl_LIBRARY: /usr/lib64/libGL.so

  and GLVND libraries for OpenGL and GLX:

    OPENGL_opengl_LIBRARY: /usr/lib64/libOpenGL.so
    OPENGL_glx_LIBRARY: /usr/lib64/libGLX.so

  OpenGL_GL_PREFERENCE has not been set to "GLVND" or "LEGACY", so for
  compatibility with CMake 3.10 and below the legacy GL library will be used.
Call Stack (most recent call first):
  avogadro/rendering/CMakeLists.txt:6 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found OpenGL: /usr/lib64/libOpenGL.so   
-- Found GLEW: /usr/include  
-- Found PythonInterp: /usr/bin/python (found suitable version "3.9.6", minimum required is "2") 
Avogadro Generators not found at /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/../avogadrogenerators!
CMake Warning (dev) at /usr/share/cmake/Modules/FindOpenGL.cmake:315 (message):
  Policy CMP0072 is not set: FindOpenGL prefers GLVND by default when
  available.  Run "cmake --help-policy CMP0072" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  FindOpenGL found both a legacy GL library:

    OPENGL_gl_LIBRARY: /usr/lib64/libGL.so

  and GLVND libraries for OpenGL and GLX:

    OPENGL_opengl_LIBRARY: /usr/lib64/libOpenGL.so
    OPENGL_glx_LIBRARY: /usr/lib64/libGLX.so

  OpenGL_GL_PREFERENCE has not been set to "GLVND" or "LEGACY", so for
  compatibility with CMake 3.10 and below the legacy GL library will be used.
Call Stack (most recent call first):
  avogadro/qtplugins/overlayaxes/CMakeLists.txt:3 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -pipe -march=native -fno-diagnostics-color -O2
C++             -pipe -march=native -fno-diagnostics-color -O2
Linker flags:
Executable      -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0
Module          -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0
Shared          -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0

-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build"
ninja -v -j4 -l0
[1/463] /usr/bin/x86_64-pc-linux-gnu-gcc  -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -MD -MT thirdparty/struct/CMakeFiles/struct.dir/struct.c.o -MF thirdparty/struct/CMakeFiles/struct.dir/struct.c.o.d -o thirdparty/struct/CMakeFiles/struct.dir/struct.c.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct/struct.c
[2/463] /usr/bin/x86_64-pc-linux-gnu-gcc  -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -MD -MT thirdparty/struct/CMakeFiles/struct.dir/struct_endian.c.o -MF thirdparty/struct/CMakeFiles/struct.dir/struct_endian.c.o.d -o thirdparty/struct/CMakeFiles/struct.dir/struct_endian.c.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct/struct_endian.c
[3/463] : && /usr/bin/cmake -E rm -f thirdparty/struct/libstruct.a && /usr/bin/x86_64-pc-linux-gnu-ar qc thirdparty/struct/libstruct.a  thirdparty/struct/CMakeFiles/struct.dir/struct.c.o thirdparty/struct/CMakeFiles/struct.dir/struct_endian.c.o && /usr/bin/x86_64-pc-linux-gnu-ranlib thirdparty/struct/libstruct.a && :
[4/463] /usr/bin/x86_64-pc-linux-gnu-g++  -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT utilities/encodefile/CMakeFiles/encodefile.dir/encodefile.cxx.o -MF utilities/encodefile/CMakeFiles/encodefile.dir/encodefile.cxx.o.d -o utilities/encodefile/CMakeFiles/encodefile.dir/encodefile.cxx.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/utilities/encodefile/encodefile.cxx
[5/463] /usr/bin/x86_64-pc-linux-gnu-gcc  -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -MD -MT thirdparty/libgwavi/CMakeFiles/libgwavi.dir/gwavi.c.o -MF thirdparty/libgwavi/CMakeFiles/libgwavi.dir/gwavi.c.o.d -o thirdparty/libgwavi/CMakeFiles/libgwavi.dir/gwavi.c.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/libgwavi/gwavi.c
[6/463] /usr/bin/x86_64-pc-linux-gnu-gcc  -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -MD -MT thirdparty/libgwavi/CMakeFiles/libgwavi.dir/fileio.c.o -MF thirdparty/libgwavi/CMakeFiles/libgwavi.dir/fileio.c.o.d -o thirdparty/libgwavi/CMakeFiles/libgwavi.dir/fileio.c.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/libgwavi/fileio.c
[7/463] : && /usr/bin/x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0    -rdynamic utilities/encodefile/CMakeFiles/encodefile.dir/encodefile.cxx.o -o bin/encodefile   && :
[8/463] /usr/bin/x86_64-pc-linux-gnu-gcc  -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -MD -MT thirdparty/libgwavi/CMakeFiles/libgwavi.dir/avi-utils.c.o -MF thirdparty/libgwavi/CMakeFiles/libgwavi.dir/avi-utils.c.o.d -o thirdparty/libgwavi/CMakeFiles/libgwavi.dir/avi-utils.c.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/libgwavi/avi-utils.c
[9/463] : && /usr/bin/cmake -E rm -f thirdparty/libgwavi/liblibgwavi.a && /usr/bin/x86_64-pc-linux-gnu-ar qc thirdparty/libgwavi/liblibgwavi.a  thirdparty/libgwavi/CMakeFiles/libgwavi.dir/gwavi.c.o thirdparty/libgwavi/CMakeFiles/libgwavi.dir/fileio.c.o thirdparty/libgwavi/CMakeFiles/libgwavi.dir/avi-utils.c.o && /usr/bin/x86_64-pc-linux-gnu-ranlib thirdparty/libgwavi/liblibgwavi.a && :
[10/463] /usr/bin/x86_64-pc-linux-gnu-g++  -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT utilities/resdata/CMakeFiles/resdataparse.dir/resdataparse.cxx.o -MF utilities/resdata/CMakeFiles/resdataparse.dir/resdataparse.cxx.o.d -o utilities/resdata/CMakeFiles/resdataparse.dir/resdataparse.cxx.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/utilities/resdata/resdataparse.cxx
[11/463] : && /usr/bin/x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0    -rdynamic utilities/resdata/CMakeFiles/resdataparse.dir/resdataparse.cxx.o -o bin/resdataparse   && :
[12/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAvogadroCore_EXPORTS -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -isystem /usr/include/eigen3  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/cube.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/cube.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/cube.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/core/cube.cpp
[13/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAvogadroCore_EXPORTS -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -isystem /usr/include/eigen3  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/coordinateblockgenerator.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/coordinateblockgenerator.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/coordinateblockgenerator.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/core/coordinateblockgenerator.cpp
[14/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAvogadroCore_EXPORTS -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -isystem /usr/include/eigen3  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/elements.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/elements.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/elements.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/core/elements.cpp
[15/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAvogadroCore_EXPORTS -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -isystem /usr/include/eigen3  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/crystaltools.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/crystaltools.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/crystaltools.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/core/crystaltools.cpp
[16/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAvogadroCore_EXPORTS -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -isystem /usr/include/eigen3  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/graph.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/graph.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/graph.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/core/graph.cpp
[17/463] /usr/bin/x86_64-pc-linux-gnu-g++  -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT utilities/bodr/CMakeFiles/bodrparse.dir/bodrparse.cxx.o -MF utilities/bodr/CMakeFiles/bodrparse.dir/bodrparse.cxx.o.d -o utilities/bodr/CMakeFiles/bodrparse.dir/bodrparse.cxx.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/utilities/bodr/bodrparse.cxx
[18/463] : && /usr/bin/x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0    -rdynamic utilities/bodr/CMakeFiles/bodrparse.dir/bodrparse.cxx.o -o bin/bodrparse   && :
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[39/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/gromacsformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/gromacsformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/gromacsformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/gromacsformat.cpp
[40/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/mdlformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/mdlformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/mdlformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/mdlformat.cpp
[41/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/cmlformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/cmlformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/cmlformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/cmlformat.cpp
[42/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/cjsonformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/cjsonformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/cjsonformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/cjsonformat.cpp
[43/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/vaspformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/vaspformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/vaspformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/vaspformat.cpp
[44/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/pdbformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/pdbformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/pdbformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/pdbformat.cpp
[45/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp
FAILED: avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o 
/usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/hdf5dataformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp
/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp: In member function ‘bool Avogadro::Io::Hdf5DataFormat::datasetExists(const string&) const’:
/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp:270:26: error: too few arguments to function ‘herr_t H5Oget_info_by_name3(hid_t, const char*, H5O_info2_t*, unsigned int, hid_t)’
  270 |   if (H5Oget_info_by_name(d->fileId, path.c_str(), &info, H5P_DEFAULT) < 0)
      |                          ^
In file included from /usr/include/H5Apublic.h:22,
                 from /usr/include/hdf5.h:23,
                 from /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp:19:
/usr/include/H5Opublic.h:557:15: note: declared here
  557 | H5_DLL herr_t H5Oget_info_by_name3(hid_t loc_id, const char *name, H5O_info2_t *oinfo, unsigned fields,
      |               ^~~~~~~~~~~~~~~~~~~~
/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > Avogadro::Io::Hdf5DataFormat::datasets() const’:
/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp:506:25: error: too few arguments to function ‘herr_t H5Ovisit3(hid_t, H5_index_t, H5_iter_order_t, H5O_iterate2_t, void*, unsigned int)’
  506 |   herr_t code = H5Ovisit(d->fileId, H5_INDEX_NAME, H5_ITER_INC,
      |                         ^
In file included from /usr/include/H5Apublic.h:22,
                 from /usr/include/hdf5.h:23,
                 from /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/hdf5dataformat.cpp:19:
/usr/include/H5Opublic.h:1326:15: note: declared here
 1326 | H5_DLL herr_t H5Ovisit3(hid_t obj_id, H5_index_t idx_type, H5_iter_order_t order, H5O_iterate2_t op,
      |               ^~~~~~~~~
[46/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/trrformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/trrformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/trrformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/trrformat.cpp
[47/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/xyzformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/xyzformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/xyzformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/xyzformat.cpp
[48/463] /usr/bin/x86_64-pc-linux-gnu-g++ -DAVO_USE_HDF5 -DAvogadroIO_EXPORTS -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/core -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/avogadro/io -isystem /usr/include/eigen3 -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/pugixml -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty/struct -isystem /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/thirdparty  -DNDEBUG -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/lammpsformat.cpp.o -MF avogadro/io/CMakeFiles/AvogadroIO.dir/lammpsformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/lammpsformat.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/io/lammpsformat.cpp
ninja: build stopped: subcommand failed.
 * ERROR: sci-libs/avogadrolibs-1.93.0::gentoo failed (compile phase):
 *   ninja -v -j4 -l0 failed
 * 
 * Call stack:
 *     ebuild.sh, line  127:  Called src_compile
 *   environment, line 2167:  Called cmake-utils_src_compile
 *   environment, line  855:  Called cmake-utils_src_make
 *   environment, line 1039:  Called _cmake_ninja_src_make
 *   environment, line  502:  Called eninja
 *   environment, line 1345:  Called die
 * The specific snippet of code:
 *       "$@" || die "${nonfatal_args[@]}" "${*} failed"
 * 
 * If you need support, post the output of `emerge --info '=sci-libs/avogadrolibs-1.93.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-libs/avogadrolibs-1.93.0::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-libs:avogadrolibs-1.93.0:20210826-170820.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build'
 * S: '/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0'