* Package: sci-chemistry/openbabel-2.4.1-r2 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux openmp 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/81ccd60f63092c825376eb6dd8897edc9eb86820 (Sun Mar 28 00:17:34 UTC 2021) @@@@@ END @@@@@ emerge --info: Portage 3.0.17 (python 3.9.2-final-0, default/linux/amd64/17.1, gcc-10.2.0, glibc-2.32-r8, 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-glibc2.32 KiB Mem: 71926568 total, 55704708 free KiB Swap: 0 total, 0 free sh bash 5.1_p4 ld GNU ld (Gentoo 2.35.2 p1) 2.35.2 app-shells/bash: 5.1_p4::gentoo dev-lang/perl: 5.32.1::gentoo dev-lang/python: 2.7.18_p7::gentoo, 3.7.10::gentoo, 3.8.8::gentoo, 3.9.2::gentoo dev-util/cmake: 3.20.0::gentoo sys-apps/baselayout: 2.7-r1::gentoo sys-apps/openrc: 0.42.1-r1::gentoo sys-apps/sandbox: 2.22::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.16.3-r1::gentoo sys-devel/binutils: 2.35.2::gentoo sys-devel/gcc: 10.2.0-r5::gentoo sys-devel/gcc-config: 2.4::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.11::gentoo (virtual/os-headers) sys-libs/glibc: 2.32-r8::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="* 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/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-chemistry/openbabel-2.4.1-r2/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 binpkg-multi-instance 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: 2021-03-28T01:18:46 >>> dev-cpp/eigen-3.3.9 2021-03-28T01:18:46 >>> sci-libs/inchi-1.04 2021-03-28T01:19:00 >>> sci-chemistry/openbabel-2.4.1-r2 >>> Unpacking source... >>> Unpacking openbabel-2.4.1.tar.gz to /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work >>> Unpacking openbabel.png to /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work unpack openbabel.png: file format not recognized. Ignoring. >>> Source unpacked in /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work >>> Preparing source in /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1 ... * Applying openbabel-2.4.1-gcc10.patch ... [ ok ] * Hardcoded definition(s) removed in CMakeLists.txt: * set(CMAKE_BUILD_TYPE RelWithDebInfo) >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build" cmake -C /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DOPENBABEL_USE_SYSTEM_INCHI=ON -DENABLE_OPENMP=yes -DBUILD_GUI=no -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1 loading initial cache file /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build/gentoo_common_config.cmake CMake Deprecation Warning at CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- 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 CMake Deprecation Warning at CMakeLists.txt:11 (cmake_policy): The OLD behavior for policy CMP0005 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at CMakeLists.txt:13 (cmake_policy): The OLD behavior for policy CMP0042 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (INCHI) does not match the name of the calling package (Inchi). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/modules/FindInchi.cmake:19 (find_package_handle_standard_args) CMakeLists.txt:143 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found INCHI: /usr/lib64/libinchi.so -- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.10") -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") -- Could NOT find wxWidgets (missing: wxWidgets_LIBRARIES wxWidgets_INCLUDE_DIRS) -- Looking for conio.h -- Looking for conio.h - not found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for time.h -- Looking for time.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for rpc/xdr.h -- Looking for rpc/xdr.h - not found -- Looking for regex.h -- Looking for regex.h - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for rint -- Looking for rint - not found -- Looking for snprintf -- Looking for snprintf - found -- Looking for sranddev -- Looking for sranddev - not found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strncasecmp -- Looking for strncasecmp - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of clock_t -- Check size of clock_t - done -- Performing Test SCANDIR_NEEDS_CONST -- Performing Test SCANDIR_NEEDS_CONST - Failed -- Performing Test HAVE_GCC_VISIBILITY -- Performing Test HAVE_GCC_VISIBILITY - Success -- Checking available shared pointer... -- Performing Test HAVE_STD_SHARED_PTR -- Performing Test HAVE_STD_SHARED_PTR - Success -- Performing Test HAVE_STD_TR1_SHARED_PTR -- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed -- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER -- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Success -- Use std::shared_ptr in memory -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Found PkgConfig: x86_64-pc-linux-gnu-pkg-config (found version "1.7.4") -- Checking for module 'cairo' -- Package 'cairo', required by 'virtual:world', not found -- Could NOT find Cairo (missing: CAIRO_LIBRARIES CAIRO_INCLUDE_DIRS) -- Could NOT find Cairo. PNG output will NOT be supported. -- Looking for getopt -- Looking for getopt - found -- GUI will not be built -- Found PythonInterp: /usr/bin/python (found version "3.9.2") CMake Deprecation Warning at scripts/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -O2 -pipe -march=x86-64 -frecord-gcc-switches -fopenmp C++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fopenmp Linker flags: Executable -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Module -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Shared -Wl,--enable-new-dtags -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-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build" ninja -v -j36 -l0 [1/472] /usr/bin/x86_64-pc-linux-gnu-g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DUSING_DYNAMIC_LIBS -Dplugin_ops_EXPORTS -Iinclude -I/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/data -I/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -fopenmp -fPIC -DOB_MODULE_PATH="\"/usr/lib64/openbabel/2.4.1\"" -MD -MT src/CMakeFiles/plugin_ops.dir/ops/addfilename.o -MF src/CMakeFiles/plugin_ops.dir/ops/addfilename.o.d -o src/CMakeFiles/plugin_ops.dir/ops/addfilename.o -c 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-DUSING_DYNAMIC_LIBS -Iinclude -I/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/data -I/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -fopenmp -fPIC -DOB_MODULE_PATH="\"/usr/lib64/openbabel/2.4.1\"" -MD -MT src/CMakeFiles/openbabel.dir/math/align.o -MF src/CMakeFiles/openbabel.dir/math/align.o.d -o src/CMakeFiles/openbabel.dir/math/align.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/math/align.cpp [165/472] /usr/bin/x86_64-pc-linux-gnu-g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DUSING_DYNAMIC_LIBS -Dtinkerformat_EXPORTS -Iinclude -I/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/data -I/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include -I/usr/include/eigen3 -I/usr/include/libxml2 -DNDEBUG -O2 -pipe -march=x86-64 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src/formats/CMakeFiles/pdbqtformat.dir/pdbqtformat.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/formats/pdbqtformat.cpp [167/472] /usr/bin/x86_64-pc-linux-gnu-g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -Iinclude -I/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/data -I/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include -I/usr/include/eigen3 -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -fopenmp -fPIC -DOB_MODULE_PATH="\"/usr/lib64/openbabel/2.4.1\"" -MD -MT src/CMakeFiles/openbabel.dir/stereo/perception.o -MF src/CMakeFiles/openbabel.dir/stereo/perception.o.d -o src/CMakeFiles/openbabel.dir/stereo/perception.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/stereo/perception.cpp /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/stereo/perception.cpp: In function ‘void OpenBabel::StereoRefToImplicit(OpenBabel::OBMol&, OpenBabel::OBStereo::Ref)’: /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/stereo/perception.cpp:2871:16: warning: ‘template class std::binder1st’ is deprecated [-Wdeprecated-declarations] 2871 | const std::binder1st > equal_to_atomId = std::bind1st (equal_to(), atomId); | ^~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/include/g++-v10/bits/stl_function.h:1392, from /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/include/g++-v10/bits/stl_tree.h:65, from /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/include/g++-v10/map:60, from /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include/openbabel/base.h:26, from /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include/openbabel/stereo/stereo.h:27, from /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include/openbabel/stereo/tetranonplanar.h:27, from /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include/openbabel/stereo/tetrahedral.h:27, from /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/stereo/perception.cpp:25: /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/include/g++-v10/backward/binders.h:108:11: note: declared here 108 | class binder1st | ^~~~~~~~~ /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/stereo/perception.cpp: In function ‘void OpenBabel::ImplicitRefToStereo(OpenBabel::OBMol&, OpenBabel::OBStereo::Ref, OpenBabel::OBStereo::Ref)’: /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/stereo/perception.cpp:2903:16: warning: ‘template class std::binder1st’ is deprecated [-Wdeprecated-declarations] 2903 | const std::binder1st > equal_to_implicitRef = std::bind1st (equal_to(), (OBStereo::Ref) OBStereo::ImplicitRef); | ^~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/include/g++-v10/bits/stl_function.h:1392, from /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/include/g++-v10/bits/stl_tree.h:65, from /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/include/g++-v10/map:60, from /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include/openbabel/base.h:26, from /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include/openbabel/stereo/stereo.h:27, from /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include/openbabel/stereo/tetranonplanar.h:27, from /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include/openbabel/stereo/tetrahedral.h:27, from /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/stereo/perception.cpp:25: /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/include/g++-v10/backward/binders.h:108:11: note: declared here 108 | class binder1st | ^~~~~~~~~ [168/472] /usr/bin/x86_64-pc-linux-gnu-g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DUSING_DYNAMIC_LIBS 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-I/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/include -I/usr/include/eigen3 -I/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/test -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -fopenmp -DOB_MODULE_PATH="\"/usr/lib64/openbabel/2.4.1\"" -DTESTDATADIR="\"/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/test/files/\"" -DFORMATDIR="\"/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build/lib64//\"" -DTESTDIR=/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/test -MD -MT test/CMakeFiles/test_runner.dir/unitcell.o -MF test/CMakeFiles/test_runner.dir/unitcell.o.d -o test/CMakeFiles/test_runner.dir/unitcell.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/test/unitcell.cpp [472/472] : && /usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fopenmp -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc 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lib64/libopenbabel.so.5.0.0 -lm -ldl -lz && : >>> Source compiled. >>> Test phase: sci-chemistry/openbabel-2.4.1-r2 >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build" cmake -C /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DOPENBABEL_USE_SYSTEM_INCHI=ON -DPYTHON_EXECUTABLE=false -DOPENMP=yes -DBUILD_GUI=no -DTESTS=yes -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1 loading initial cache file /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build/gentoo_common_config.cmake CMake Deprecation Warning at CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at CMakeLists.txt:11 (cmake_policy): The OLD behavior for policy CMP0005 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at CMakeLists.txt:13 (cmake_policy): The OLD behavior for policy CMP0042 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Could NOT find wxWidgets (missing: wxWidgets_LIBRARIES wxWidgets_INCLUDE_DIRS) -- Checking available shared pointer... -- Use std::shared_ptr in memory -- Checking for module 'cairo' -- Package 'cairo', required by 'virtual:world', not found -- Could NOT find Cairo (missing: CAIRO_LIBRARIES CAIRO_INCLUDE_DIRS) -- Could NOT find Cairo. PNG output will NOT be supported. -- GUI will not be built -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) CMake Deprecation Warning at scripts/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -O2 -pipe -march=x86-64 -frecord-gcc-switches -fopenmp C++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fopenmp Linker flags: Executable -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Module -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Shared -Wl,--enable-new-dtags -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: OPENMP TESTS -- Build files have been written to: /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build" ninja -v -j36 -l0 ninja: no work to do. >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build" ctest -j 36 --test-load 999 -E py Test project /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build Start 1: test_align_1 Start 2: test_align_2 Start 3: test_align_3 Start 4: test_align_4 Start 5: test_align_5 Start 6: test_automorphism_1 Start 7: test_automorphism_2 Start 8: test_automorphism_3 Start 9: test_automorphism_4 Start 10: test_automorphism_5 Start 11: test_automorphism_6 Start 12: test_automorphism_7 Start 13: test_automorphism_8 Start 14: test_automorphism_9 Start 15: test_automorphism_10 Start 16: test_builder_1 Start 17: test_builder_2 Start 18: test_builder_3 Start 19: test_builder_4 Start 20: test_builder_5 Start 21: test_canonconsistent_1 Start 22: test_canonconsistent_2 Start 23: test_canonconsistent_3 Start 24: test_canonstable_1 Start 25: test_carspacegroup_1 Start 26: test_carspacegroup_2 Start 27: test_carspacegroup_3 Start 28: test_carspacegroup_4 Start 29: test_cifspacegroup_1 Start 30: test_cifspacegroup_2 Start 31: test_cifspacegroup_3 Start 32: test_cifspacegroup_4 Start 33: test_cistrans_1 Start 34: test_cistrans_2 Start 35: test_cistrans_3 Start 36: test_cistrans_4 1/150 Test #1: test_align_1 ..................... Passed 0.07 sec Start 37: test_cistrans_5 2/150 Test #2: test_align_2 ..................... Passed 0.08 sec Start 38: test_cistrans_6 3/150 Test #3: test_align_3 ..................... Passed 0.10 sec Start 39: test_cistrans_7 4/150 Test #4: test_align_4 ..................... Passed 0.13 sec Start 40: test_cistrans_8 5/150 Test #5: test_align_5 ..................... Passed 0.15 sec Start 41: test_cistrans_9 6/150 Test #6: test_automorphism_1 .............. Passed 0.16 sec Start 42: test_graphsym_1 7/150 Test #7: test_automorphism_2 .............. Passed 0.17 sec Start 43: test_graphsym_2 8/150 Test #8: test_automorphism_3 .............. Passed 0.19 sec Start 44: test_graphsym_3 9/150 Test #9: test_automorphism_4 .............. Passed 0.21 sec Start 45: test_graphsym_4 10/150 Test #10: test_automorphism_5 .............. Passed 0.22 sec Start 46: test_graphsym_5 11/150 Test #11: test_automorphism_6 .............. Passed 0.23 sec Start 47: test_gzip_1 12/150 Test #12: test_automorphism_7 .............. Passed 0.25 sec Start 48: test_implicitH_1 13/150 Test #13: test_automorphism_8 .............. Passed 0.26 sec Start 49: test_lssr_1 14/150 Test #14: test_automorphism_9 .............. Passed 0.27 sec Start 50: test_lssr_2 15/150 Test #15: test_automorphism_10 ............. Passed 0.27 sec Start 51: test_lssr_3 16/150 Test #22: test_canonconsistent_2 ........... Passed 0.29 sec Start 52: test_lssr_4 17/150 Test #25: test_carspacegroup_1 ............. Passed 0.31 sec Start 53: test_lssr_5 18/150 Test #31: test_cifspacegroup_3 ............. Passed 0.31 sec Start 54: test_isomorphism_1 19/150 Test #33: test_cistrans_1 .................. Passed 0.31 sec Start 55: test_isomorphism_2 20/150 Test #34: test_cistrans_2 .................. Passed 0.33 sec Start 56: test_isomorphism_3 21/150 Test #35: test_cistrans_3 .................. Passed 0.35 sec Start 57: test_isomorphism_4 22/150 Test #18: test_builder_3 ................... Passed 0.42 sec Start 58: test_isomorphism_5 23/150 Test #19: test_builder_4 ................... Passed 0.44 sec Start 59: test_isomorphism_6 24/150 Test #20: test_builder_5 ................... Passed 0.45 sec Start 60: test_isomorphism_7 25/150 Test #23: test_canonconsistent_3 ........... Passed 0.45 sec Start 61: test_isomorphism_8 26/150 Test #36: test_cistrans_4 .................. Passed 0.46 sec Start 62: test_multicml_1 27/150 Test #21: test_canonconsistent_1 ........... Passed 0.50 sec Start 63: test_regressions_1 28/150 Test #26: test_carspacegroup_2 ............. Passed 0.51 sec Start 64: test_regressions_221 29/150 Test #29: test_cifspacegroup_1 ............. Passed 0.52 sec Start 65: test_regressions_222 30/150 Test #32: test_cifspacegroup_4 ............. Passed 0.55 sec Start 66: test_regressions_223 31/150 Test #28: test_carspacegroup_4 ............. Passed 0.58 sec Start 67: test_regressions_224 32/150 Test #37: test_cistrans_5 .................. Passed 0.57 sec Start 68: test_rotor_1 33/150 Test #38: test_cistrans_6 .................. Passed 0.55 sec Start 69: test_rotor_2 34/150 Test #39: test_cistrans_7 .................. Passed 0.55 sec Start 70: test_rotor_3 35/150 Test #40: test_cistrans_8 .................. Passed 0.54 sec Start 71: test_rotor_4 36/150 Test #41: test_cistrans_9 .................. Passed 0.53 sec Start 72: test_shuffle_1 37/150 Test #42: test_graphsym_1 .................. Passed 0.54 sec Start 73: test_shuffle_2 38/150 Test #43: test_graphsym_2 .................. Passed 0.55 sec Start 74: test_shuffle_3 39/150 Test #44: test_graphsym_3 .................. Passed 0.55 sec Start 75: test_shuffle_4 40/150 Test #45: test_graphsym_4 .................. Passed 0.54 sec Start 76: test_shuffle_5 41/150 Test #46: test_graphsym_5 .................. Passed 0.57 sec Start 77: test_smiles_1 42/150 Test #48: test_implicitH_1 ................. Passed 0.57 sec Start 78: test_smiles_2 43/150 Test #49: test_lssr_1 ...................... Passed 0.59 sec Start 79: test_smiles_3 44/150 Test #53: test_lssr_5 ...................... Passed 0.55 sec Start 80: test_spectrophore_1 45/150 Test #54: test_isomorphism_1 ............... Passed 0.56 sec Start 81: test_spectrophore_2 46/150 Test #55: test_isomorphism_2 ............... Passed 0.57 sec Start 82: test_spectrophore_3 47/150 Test #56: test_isomorphism_3 ............... Passed 0.56 sec Start 83: test_spectrophore_4 48/150 Test #47: test_gzip_1 ...................... Passed 0.71 sec Start 84: test_spectrophore_5 49/150 Test #57: test_isomorphism_4 ............... Passed 0.56 sec Start 85: test_squareplanar_1 50/150 Test #30: test_cifspacegroup_2 ............. Passed 0.94 sec Start 86: test_squareplanar_2 51/150 Test #27: test_carspacegroup_3 ............. Passed 0.96 sec Start 87: test_squareplanar_3 52/150 Test #58: test_isomorphism_5 ............... Passed 0.56 sec Start 88: test_squareplanar_4 53/150 Test #59: test_isomorphism_6 ............... Passed 0.55 sec Start 89: test_squareplanar_5 54/150 Test #60: test_isomorphism_7 ............... Passed 0.54 sec Start 90: test_stereo_1 55/150 Test #61: test_isomorphism_8 ............... Passed 0.55 sec Start 91: test_stereo_2 56/150 Test #62: test_multicml_1 .................. Passed 0.53 sec Start 92: test_stereo_3 57/150 Test #63: test_regressions_1 ............... Passed 0.52 sec Start 93: test_stereo_4 58/150 Test #64: test_regressions_221 ............. Passed 0.53 sec Start 94: test_stereo_5 59/150 Test #65: test_regressions_222 ............. Passed 0.53 sec Start 95: test_stereo_6 60/150 Test #66: test_regressions_223 ............. Passed 0.53 sec Start 96: test_stereoperception_1 61/150 Test #67: test_regressions_224 ............. Passed 0.50 sec Start 97: test_stereoperception_2 62/150 Test #68: test_rotor_1 ..................... Passed 0.51 sec Start 98: test_stereoperception_3 63/150 Test #69: test_rotor_2 ..................... Passed 0.53 sec Start 99: test_stereoperception_4 64/150 Test #70: test_rotor_3 ..................... Passed 0.54 sec Start 100: test_tautomer_1 65/150 Test #71: test_rotor_4 ..................... Passed 0.55 sec Start 101: test_tautomer_2 66/150 Test #75: test_shuffle_4 ................... Passed 0.50 sec Start 102: test_tetrahedral_1 67/150 Test #77: test_smiles_1 .................... Passed 0.46 sec Start 103: test_tetrahedral_2 68/150 Test #78: test_smiles_2 .................... Passed 0.43 sec Start 104: test_tetrahedral_3 69/150 Test #79: test_smiles_3 .................... Passed 0.41 sec Start 105: test_tetrahedral_4 70/150 Test #81: test_spectrophore_2 .............. Passed 0.39 sec Start 106: test_tetrahedral_5 71/150 Test #52: test_lssr_4 ...................... Passed 0.99 sec Start 107: test_tetranonplanar_1 72/150 Test #74: test_shuffle_3 ................... Passed 0.61 sec Start 108: test_tetraplanar_1 73/150 Test #76: test_shuffle_5 ................... Passed 0.61 sec Start 109: test_uniqueid_1 74/150 Test #80: test_spectrophore_1 .............. Passed 0.51 sec Start 110: test_uniqueid_2 75/150 Test #82: test_spectrophore_3 .............. Passed 0.50 sec Start 111: test_aromatest_1 76/150 Test #83: test_spectrophore_4 .............. Passed 0.52 sec Start 112: test_atom_1 77/150 Test #84: test_spectrophore_5 .............. Passed 0.52 sec Start 113: test_atom_2 78/150 Test #85: test_squareplanar_1 .............. Passed 0.52 sec Start 114: test_atom_3 79/150 Test #86: test_squareplanar_2 .............. Passed 0.52 sec Start 115: test_atom_4 80/150 Test #87: test_squareplanar_3 .............. Passed 0.52 sec Start 116: test_bond_1 81/150 Test #88: test_squareplanar_4 .............. Passed 0.52 sec Start 117: test_cansmi_1 82/150 Test #89: test_squareplanar_5 .............. Passed 0.53 sec Start 118: test_charge_mmff94_1 83/150 Test #90: test_stereo_1 .................... Passed 0.54 sec Start 119: test_charge_gasteiger_1 84/150 Test #91: test_stereo_2 .................... Passed 0.54 sec Start 120: test_conversion_1 85/150 Test #92: test_stereo_3 .................... Passed 0.55 sec Start 121: test_datatest_1 86/150 Test #93: test_stereo_4 .................... Passed 0.57 sec Start 122: test_ffgaff_1 87/150 Test #94: test_stereo_5 .................... Passed 0.57 sec Start 123: test_ffghemical_1 88/150 Test #96: test_stereoperception_1 .......... Passed 0.54 sec Start 124: test_ffmmff94_1 89/150 Test #97: test_stereoperception_2 .......... Passed 0.54 sec Start 125: test_ffmmff94_2 90/150 Test #98: test_stereoperception_3 .......... Passed 0.53 sec Start 126: test_ffuff_1 91/150 Test #99: test_stereoperception_4 .......... Passed 0.54 sec Start 127: test_formalcharge_1 92/150 Test #100: test_tautomer_1 .................. Passed 0.52 sec Start 128: test_format_1 93/150 Test #102: test_tetrahedral_1 ............... Passed 0.49 sec Start 129: test_formula_1 94/150 Test #103: test_tetrahedral_2 ............... Passed 0.50 sec Start 130: test_internalcoord_1 95/150 Test #104: test_tetrahedral_3 ............... Passed 0.50 sec Start 131: test_invalidsmarts_1 96/150 Test #105: test_tetrahedral_4 ............... Passed 0.51 sec Start 132: test_invalidsmiles_1 97/150 Test #72: test_shuffle_1 ................... Passed 1.13 sec Start 133: test_iterators_1 98/150 Test #73: test_shuffle_2 ................... Passed 1.15 sec Start 134: test_logp_psa_1 99/150 Test #95: test_stereo_6 .................... Passed 0.78 sec Start 135: test_math_1 100/150 Test #106: test_tetrahedral_5 ............... Passed 0.60 sec Start 136: test_math_2 101/150 Test #101: test_tautomer_2 .................. Passed 0.72 sec Start 137: test_math_3 102/150 Test #51: test_lssr_3 ...................... Passed 1.67 sec Start 138: test_math_4 103/150 Test #107: test_tetranonplanar_1 ............ Passed 0.67 sec Start 139: test_mol_1 104/150 Test #108: test_tetraplanar_1 ............... Passed 0.67 sec Start 140: test_phmodel_1 105/150 Test #109: test_uniqueid_1 .................. Passed 0.68 sec Start 141: test_residue_1 106/150 Test #110: test_uniqueid_2 .................. Passed 0.68 sec Start 142: test_ringtest_1 107/150 Test #111: test_aromatest_1 ................. Passed 0.69 sec Start 143: test_smartstest_1 108/150 Test #112: test_atom_1 ...................... Passed 0.70 sec Start 144: test_smartsparse_1 109/150 Test #113: test_atom_2 ...................... Passed 0.71 sec Start 145: test_smilesmatch_1 110/150 Test #114: test_atom_3 ...................... Passed 0.72 sec Start 146: test_unitcell_1 111/150 Test #115: test_atom_4 ...................... Passed 0.74 sec Start 147: test_cmlreadfile_1 112/150 Test #116: test_bond_1 ...................... Passed 0.75 sec Start 148: inchiSamples.sdf_Test 113/150 Test #119: test_charge_gasteiger_1 .......... Passed 0.74 sec Start 149: inchiSamplesTechMan.sdf_Test 114/150 Test #120: test_conversion_1 ................ Passed 0.76 sec Start 150: inchiSteffen_PubChem.smi_Test 115/150 Test #121: test_datatest_1 .................. Passed 0.76 sec 116/150 Test #128: test_format_1 .................... Passed 0.66 sec 117/150 Test #130: test_internalcoord_1 ............. Passed 0.62 sec 118/150 Test #131: test_invalidsmarts_1 ............. Passed 0.61 sec 119/150 Test #118: test_charge_mmff94_1 ............. Passed 0.84 sec 120/150 Test #127: test_formalcharge_1 .............. Passed 0.68 sec 121/150 Test #129: test_formula_1 ................... Passed 0.64 sec 122/150 Test #132: test_invalidsmiles_1 ............. Passed 0.59 sec 123/150 Test #133: test_iterators_1 ................. Passed 0.56 sec 124/150 Test #134: test_logp_psa_1 .................. Passed 0.52 sec 125/150 Test #137: test_math_3 ...................... Passed 0.60 sec 126/150 Test #139: test_mol_1 ....................... Passed 0.57 sec 127/150 Test #140: test_phmodel_1 ................... Passed 0.56 sec 128/150 Test #141: test_residue_1 ................... Passed 0.52 sec 129/150 Test #144: test_smartsparse_1 ............... Passed 0.43 sec 130/150 Test #146: test_unitcell_1 .................. Passed 0.38 sec 131/150 Test #147: test_cmlreadfile_1 ............... Passed 0.35 sec 132/150 Test #135: test_math_1 ...................... Passed 0.72 sec 133/150 Test #136: test_math_2 ...................... Passed 0.71 sec 134/150 Test #149: inchiSamplesTechMan.sdf_Test ..... Passed 0.33 sec 135/150 Test #150: inchiSteffen_PubChem.smi_Test .... Passed 0.31 sec 136/150 Test #138: test_math_4 ...................... Passed 0.67 sec 137/150 Test #143: test_smartstest_1 ................ Passed 0.59 sec 138/150 Test #142: test_ringtest_1 .................. Passed 0.68 sec 139/150 Test #148: inchiSamples.sdf_Test ............ Passed 0.50 sec 140/150 Test #126: test_ffuff_1 ..................... Passed 1.78 sec 141/150 Test #117: test_cansmi_1 .................... Passed 2.40 sec 142/150 Test #145: test_smilesmatch_1 ............... Passed 2.14 sec 143/150 Test #122: test_ffgaff_1 .................... Passed 3.08 sec 144/150 Test #123: test_ffghemical_1 ................ Passed 3.64 sec 145/150 Test #50: test_lssr_2 ...................... Passed 5.85 sec 146/150 Test #24: test_canonstable_1 ............... Passed 26.02 sec 147/150 Test #125: test_ffmmff94_2 .................. Passed 569.83 sec 148/150 Test #17: test_builder_2 ...................***Timeout 1500.01 sec 149/150 Test #16: test_builder_1 ...................***Timeout 1500.02 sec 150/150 Test #124: test_ffmmff94_1 .................. Passed 1498.49 sec 99% tests passed, 2 tests failed out of 150 Total Test time (real) = 1500.16 sec The following tests FAILED: 16 - test_builder_1 (Timeout) 17 - test_builder_2 (Timeout) Errors while running CTest Output from these tests are in: /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build/Testing/Temporary/LastTest.log Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely. * ERROR: sci-chemistry/openbabel-2.4.1-r2::gentoo failed (test phase): * Tests failed. When you file a bug, please attach the following file: * /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build/Testing/Temporary/LastTest.log * * Call stack: * ebuild.sh, line 125: Called src_test * environment, line 2703: Called cmake-utils_src_test '-E' 'py' * environment, line 1069: Called die * The specific snippet of code: * die "Tests failed. When you file a bug, please attach the following file: * ${BUILD_DIR}/Testing/Temporary/LastTest.log"; * * If you need support, post the output of `emerge --info '=sci-chemistry/openbabel-2.4.1-r2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/openbabel-2.4.1-r2::gentoo'`. * The complete build log is located at '/var/log/emerge-log/build/sci-chemistry/openbabel-2.4.1-r2:20210328-001938.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1_build' * S: '/var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1'