* Package: sci-libs/avogadrolibs-1.93.0 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux test userland_GNU * FEATURES: network-sandbox preserve-libs sandbox test userpriv usersandbox @@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; This ebuild was merged at the following commit: https://github.com/gentoo/gentoo/commit/8f3d440fe8c354763fb8623743a6b6078d5eac5a (Sun Jan 17 11:51:38 UTC 2021) @@@@@ END @@@@@ emerge --info: Portage 3.0.13 (python 3.7.9-final-0, default/linux/amd64/17.1, gcc-10.2.0, glibc-2.32-r7, 5.4.0-1029-aws x86_64) ================================================================= System uname: Linux-5.4.0-1029-aws-x86_64-Intel-R-_Xeon-R-_Platinum_8124M_CPU_@_3.00GHz-with-gentoo-2.7 KiB Mem: 71926568 total, 57214928 free KiB Swap: 0 total, 0 free sh bash 5.1_p4 ld GNU ld (Gentoo 2.35.1 p2) 2.35.1 app-shells/bash: 5.1_p4::gentoo dev-lang/perl: 5.32.0-r1::gentoo dev-lang/python: 2.7.18-r5::gentoo, 3.7.9-r1::gentoo, 3.8.7::gentoo, 3.9.1::gentoo dev-util/cmake: 3.19.3::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.7-r1::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.20::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.16.3-r1::gentoo sys-devel/binutils: 2.35.1-r1::gentoo sys-devel/gcc: 10.2.0-r5::gentoo sys-devel/gcc-config: 2.3.2-r1::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.10::gentoo (virtual/os-headers) sys-libs/glibc: 2.32-r7::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-jobs: 1 sync-rsync-extra-opts: sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 24 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* BSD GPL-2+" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches" DISTDIR="/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/distdir" EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j36" PKGDIR="/root/.packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="acl amd64 berkdb bzip2 cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd test unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" USERLAND="GNU" Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS emerge history: 2021-01-17T15:50:32 >>> dev-qt/qtchooser-66 2021-01-17T15:50:32 >>> dev-libs/lzo-2.10 2021-01-17T15:50:32 >>> media-fonts/liberation-fonts-2.1.2 2021-01-17T15:50:33 >>> x11-misc/util-macros-1.19.2-r2 2021-01-17T15:50:33 >>> media-libs/libpng-1.6.37-r2 2021-01-17T15:50:33 >>> x11-base/xorg-proto-2020.1 2021-01-17T15:50:33 >>> x11-libs/xtrans-1.4.0 2021-01-17T15:50:34 >>> dev-cpp/eigen-3.3.9 2021-01-17T15:50:34 >>> dev-libs/libevdev-1.10.0 2021-01-17T15:50:34 >>> media-gfx/graphite2-1.3.14 2021-01-17T15:50:34 >>> sys-libs/binutils-libs-2.35.1-r1 2021-01-17T15:50:34 >>> x11-libs/pixman-0.40.0 2021-01-17T15:50:35 >>> dev-libs/double-conversion-3.1.5 2021-01-17T15:50:35 >>> media-fonts/font-util-1.3.2-r1 2021-01-17T15:50:35 >>> app-text/docbook-xml-dtd-4.3-r2 2021-01-17T15:50:33 >>> sys-libs/mtdev-1.1.6 2021-01-17T15:50:36 >>> dev-python/mako-1.1.4 2021-01-17T15:50:35 >>> x11-base/xcb-proto-1.14.1 2021-01-17T15:50:35 >>> sci-libs/spglib-1.14.1 2021-01-17T15:50:36 >>> dev-libs/libsodium-1.0.18 2021-01-17T15:50:54 >>> virtual/ttf-fonts-1-r1 2021-01-17T15:50:57 >>> media-libs/freetype-2.10.4 2021-01-17T15:50:58 >>> x11-libs/gdk-pixbuf-2.42.2 2021-01-17T15:50:59 >>> x11-libs/libXau-1.0.9-r1 2021-01-17T15:50:59 >>> x11-libs/libXdmcp-1.1.3 2021-01-17T15:51:00 >>> x11-libs/libxshmfence-1.3-r2 2021-01-17T15:51:01 >>> x11-libs/libICE-1.0.10 2021-01-17T15:51:16 >>> x11-libs/libpciaccess-0.16 2021-01-17T15:51:14 >>> dev-qt/qtcore-5.15.2-r2 2021-01-17T15:51:19 >>> dev-libs/libinput-1.16.4 2021-01-17T15:51:36 >>> media-libs/fontconfig-2.13.1-r2 2021-01-17T15:51:38 >>> dev-util/gtk-update-icon-cache-3.24.24 2021-01-17T15:51:41 >>> x11-misc/compose-tables-1.7.0 2021-01-17T15:51:41 >>> x11-libs/libxcb-1.14 2021-01-17T15:51:44 >>> x11-libs/libSM-1.2.3-r1 2021-01-17T15:51:46 >>> x11-libs/libdrm-2.4.103 2021-01-17T15:51:50 >>> dev-qt/qtnetwork-5.15.2-r1 2021-01-17T15:52:02 >>> app-eselect/eselect-fontconfig-1.1-r1 2021-01-17T15:52:07 >>> x11-libs/libX11-1.7.0 2021-01-17T15:52:07 >>> x11-libs/xcb-util-renderutil-0.3.9-r3 2021-01-17T15:52:07 >>> x11-libs/xcb-util-keysyms-0.4.0-r2 2021-01-17T15:52:08 >>> x11-libs/xcb-util-wm-0.4.1-r3 2021-01-17T15:52:08 >>> x11-libs/libxkbcommon-1.0.3 2021-01-17T15:51:33 >>> net-libs/zeromq-4.3.3 2021-01-17T15:52:21 >>> x11-libs/libXext-1.3.4 2021-01-17T15:52:22 >>> x11-libs/libXrender-0.9.10-r2 2021-01-17T15:52:22 >>> x11-libs/libXfixes-5.0.3-r3 2021-01-17T15:52:26 >>> x11-libs/xcb-util-0.4.0-r2 2021-01-17T15:52:34 >>> media-libs/libglvnd-1.3.2-r2 2021-01-17T15:52:34 >>> x11-libs/libXxf86vm-1.1.4-r2 2021-01-17T15:52:35 >>> x11-libs/libXrandr-1.5.2 2021-01-17T15:52:36 >>> x11-libs/cairo-1.16.0-r4 2021-01-17T15:52:38 >>> x11-libs/xcb-util-image-0.4.0-r2 2021-01-17T15:52:32 >>> net-libs/cppzmq-4.6.0 2021-01-17T15:52:50 >>> media-libs/harfbuzz-2.7.4 2021-01-17T15:52:48 >>> media-libs/mesa-21.0.0_rc1 2021-01-17T15:52:51 >>> x11-libs/xcb-util-cursor-0.1.3-r3 2021-01-17T15:52:59 >>> virtual/opengl-7.0-r2 2021-01-17T15:53:03 >>> dev-qt/qtgui-5.15.2-r1 2021-01-17T15:53:09 >>> dev-qt/qtwidgets-5.15.2 2021-01-17T15:53:12 >>> sci-chemistry/molequeue-0.9.0-r1 2021-01-17T15:53:35 >>> sci-libs/avogadrolibs-1.93.0 2021-01-17T15:53:54 >>> dev-cpp/gtest-1.10.0_p20200702 >>> 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=no -DENABLE_TRANSLATIONS=no -DUSE_OPENGL=no -DUSE_QT=no -DBUILD_STATIC_PLUGINS=ON -DENABLE_TESTING=yes -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 10.2.0 -- The CXX compiler identification is GNU 10.2.0 -- 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 "2.30.0") -- 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 GTest: /usr/lib64/libgtest.so -- Looking for C++ include gtest/gtest.h -- Looking for C++ include gtest/gtest.h - found -- Looking for GTEST_HAS_PTHREAD -- Looking for GTEST_HAS_PTHREAD - found -- Looking for GTEST_IS_THREADSAFE -- Looking for GTEST_IS_THREADSAFE - found -- GTest claims it has pthreads, we need to link to it. -- Found Threads: TRUE -- Adding Array test. -- Adding Atom test. -- Adding AtomTyper test. -- Adding BasisSet test. -- Adding Bond test. -- Adding CoordinateBlockGenerator test. -- Adding CoordinateSet test. -- Adding Cube test. -- Adding Eigen test. -- Adding Element test. -- Adding Graph test. -- Adding Mesh test. -- Adding Molecule test. -- Adding Mutex test. -- Adding RingPerceiver test. -- Adding Spacegroup test. -- Adding Utilities test. -- Adding UnitCell test. -- Adding Variant test. -- Adding VariantMap test. -- Test source files: arraytest.cpp;atomtest.cpp;atomtypertest.cpp;basissettest.cpp;bondtest.cpp;coordinateblockgeneratortest.cpp;coordinatesettest.cpp;cubetest.cpp;eigentest.cpp;elementtest.cpp;graphtest.cpp;meshtest.cpp;moleculetest.cpp;mutextest.cpp;ringperceivertest.cpp;spacegrouptest.cpp;utilitiestest.cpp;unitcelltest.cpp;varianttest.cpp;variantmaptest.cpp No data root found, please set to run the tests. -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -O2 -pipe -march=x86-64 -frecord-gcc-switches C++ -O2 -pipe -march=x86-64 -frecord-gcc-switches 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 CMake Warning: Manually-specified variables were not used by the project: BUILD_GPL_PLUGINS BUILD_STATIC_PLUGINS -- 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 -j36 -l0 [1/81] /usr/bin/x86_64-pc-linux-gnu-gcc -I. -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -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 [2/81] /usr/bin/x86_64-pc-linux-gnu-g++ -DAvogadroCore_EXPORTS -I. -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -Iavogadro/core -isystem /usr/include/eigen3 -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/version.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/version.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/version.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/core/version.cpp [3/81] /usr/bin/x86_64-pc-linux-gnu-gcc -I. -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -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 [4/81] : && /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 && : [5/81] /usr/bin/x86_64-pc-linux-gnu-g++ -DAvogadroCore_EXPORTS -I. -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -Iavogadro/core -isystem /usr/include/eigen3 -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/mutex.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/mutex.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/mutex.cpp.o -c /var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0/avogadro/core/mutex.cpp [6/81] /usr/bin/x86_64-pc-linux-gnu-g++ -I. -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -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 [7/81] : && /usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -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 && : [8/81] /usr/bin/x86_64-pc-linux-gnu-g++ -DAvogadroCore_EXPORTS -I. -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -Iavogadro/core -isystem /usr/include/eigen3 -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -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 [9/81] /usr/bin/x86_64-pc-linux-gnu-g++ -DAvogadroCore_EXPORTS -I. -I/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0 -Iavogadro/core -isystem /usr/include/eigen3 -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/elements.cpp.o -MF 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tests/core/CMakeFiles/AvogadroTests.dir/ringperceivertest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/spacegrouptest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/utilitiestest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/unitcelltest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/varianttest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/variantmaptest.cpp.o -o bin/AvogadroTests -Wl,-rpath,/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/lib lib/libAvogadroCore.so.1.93.0 /usr/lib64/libgtest.so /usr/lib64/libgtest_main.so -lpthread && : FAILED: bin/AvogadroTests : && /usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -rdynamic tests/core/CMakeFiles/AvogadroTests.dir/arraytest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/atomtest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/atomtypertest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/basissettest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/bondtest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/coordinateblockgeneratortest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/coordinatesettest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/cubetest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/eigentest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/elementtest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/graphtest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/meshtest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/moleculetest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/mutextest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/ringperceivertest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/spacegrouptest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/utilitiestest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/unitcelltest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/varianttest.cpp.o tests/core/CMakeFiles/AvogadroTests.dir/variantmaptest.cpp.o -o bin/AvogadroTests -Wl,-rpath,/var/tmp/portage/sci-libs/avogadrolibs-1.93.0/work/avogadrolibs-1.93.0_build/lib lib/libAvogadroCore.so.1.93.0 /usr/lib64/libgtest.so /usr/lib64/libgtest_main.so -lpthread && : /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: tests/core/CMakeFiles/AvogadroTests.dir/spacegrouptest.cpp.o: in function `SpaceGroupTest_getSpaceGroup_Test::TestBody()': spacegrouptest.cpp:(.text+0x566): undefined reference to `Avogadro::Core::AvoSpglib::getHallNumber(Avogadro::Core::Molecule const&, double)' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: tests/core/CMakeFiles/AvogadroTests.dir/spacegrouptest.cpp.o: in function `SpaceGroupTest_reduceToPrimitive_Test::TestBody()': spacegrouptest.cpp:(.text+0x1f60): undefined reference to `Avogadro::Core::AvoSpglib::reduceToPrimitive(Avogadro::Core::Molecule&, double)' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: tests/core/CMakeFiles/AvogadroTests.dir/spacegrouptest.cpp.o: in function `SpaceGroupTest_conventionalizeCell_Test::TestBody()': spacegrouptest.cpp:(.text+0x3540): undefined reference to `Avogadro::Core::AvoSpglib::conventionalizeCell(Avogadro::Core::Molecule&, double)' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: tests/core/CMakeFiles/AvogadroTests.dir/spacegrouptest.cpp.o: in function `SpaceGroupTest_fillUnitCell_Test::TestBody()': spacegrouptest.cpp:(.text+0x3ae2): undefined reference to `Avogadro::Core::AvoSpglib::getHallNumber(Avogadro::Core::Molecule const&, double)' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: spacegrouptest.cpp:(.text+0x3e29): undefined reference to `Avogadro::Core::AvoSpglib::getHallNumber(Avogadro::Core::Molecule const&, double)' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: spacegrouptest.cpp:(.text+0x468d): undefined reference to `Avogadro::Core::AvoSpglib::getHallNumber(Avogadro::Core::Molecule const&, double)' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: tests/core/CMakeFiles/AvogadroTests.dir/spacegrouptest.cpp.o: in function `SpaceGroupTest_reduceToAsymmetricUnit_Test::TestBody()': spacegrouptest.cpp:(.text+0x52b3): undefined reference to `Avogadro::Core::AvoSpglib::getHallNumber(Avogadro::Core::Molecule const&, double)' collect2: error: ld returned 1 exit status [76/81] /usr/bin/cmake -E cmake_symlink_library lib/libAvogadroIO.so.1.93.0 lib/libAvogadroIO.so.1 lib/libAvogadroIO.so && : ninja: build stopped: subcommand failed. * ERROR: sci-libs/avogadrolibs-1.93.0::gentoo failed (compile phase): * ninja -v -j36 -l0 failed * * Call stack: * ebuild.sh, line 125: Called src_compile * environment, line 2219: Called cmake-utils_src_compile * environment, line 794: Called cmake-utils_src_make * environment, line 978: Called _cmake_ninja_src_make * environment, line 526: Called eninja * environment, line 1284: 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/emerge-log/build/sci-libs/avogadrolibs-1.93.0:20210117-145356.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'