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Gentoo's Bugzilla – Attachment 695223 Details for
Bug 778851
sci-chemistry/openbabel-2.4.1-r2 fails tests
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build.log
build.log (text/plain), 376.14 KB, created by
Agostino Sarubbo
on 2021-03-28 07:00:17 UTC
(
hide
)
Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2021-03-28 07:00:17 UTC
Size:
376.14 KB
patch
obsolete
> * 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 <min> value or use a ...<max> 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 <min> value or use a ...<max> 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 /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/ops/addfilename.cpp >[2/472] /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/addinindex.o -MF src/CMakeFiles/plugin_ops.dir/ops/addinindex.o.d -o src/CMakeFiles/plugin_ops.dir/ops/addinindex.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/ops/addinindex.cpp >[3/472] /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/loader.o -MF src/CMakeFiles/plugin_ops.dir/ops/loader.o.d -o src/CMakeFiles/plugin_ops.dir/ops/loader.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/ops/loader.cpp >[4/472] /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/gen2D.o -MF src/CMakeFiles/plugin_ops.dir/ops/gen2D.o.d -o src/CMakeFiles/plugin_ops.dir/ops/gen2D.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/ops/gen2D.cpp >[5/472] /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/delnonpolarh.o -MF src/CMakeFiles/plugin_ops.dir/ops/delnonpolarh.o.d -o src/CMakeFiles/plugin_ops.dir/ops/delnonpolarh.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/ops/delnonpolarh.cpp >[6/472] /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/addpolarh.o -MF src/CMakeFiles/plugin_ops.dir/ops/addpolarh.o.d -o src/CMakeFiles/plugin_ops.dir/ops/addpolarh.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/ops/addpolarh.cpp >[7/472] /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/addnonpolarh.o -MF src/CMakeFiles/plugin_ops.dir/ops/addnonpolarh.o.d -o src/CMakeFiles/plugin_ops.dir/ops/addnonpolarh.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/ops/addnonpolarh.cpp >[8/472] /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 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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/usr/include/libxml2 -DNDEBUG -O2 -pipe -march=x86-64 -frecord-gcc-switches -fopenmp -fPIC -DOB_MODULE_PATH="\"/usr/lib64/openbabel/2.4.1\"" -MD -MT src/formats/CMakeFiles/inchiformat.dir/getinchi.o -MF src/formats/CMakeFiles/inchiformat.dir/getinchi.o.d -o src/formats/CMakeFiles/inchiformat.dir/getinchi.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/formats/getinchi.cpp >[164/472] /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/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 -frecord-gcc-switches -fopenmp -fPIC -DOB_MODULE_PATH="\"/usr/lib64/openbabel/2.4.1\"" -MD -MT src/formats/CMakeFiles/tinkerformat.dir/tinkerformat.o -MF src/formats/CMakeFiles/tinkerformat.dir/tinkerformat.o.d -o src/formats/CMakeFiles/tinkerformat.dir/tinkerformat.o -c /var/tmp/portage/sci-chemistry/openbabel-2.4.1-r2/work/openbabel-2.4.1/src/formats/tinkerformat.cpp >[166/472] /usr/bin/x86_64-pc-linux-gnu-g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER -DUSING_DYNAMIC_LIBS -Dpdbqtformat_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 -frecord-gcc-switches -fopenmp -fPIC -DOB_MODULE_PATH="\"/usr/lib64/openbabel/2.4.1\"" -MD -MT src/formats/CMakeFiles/pdbqtformat.dir/pdbqtformat.o -MF src/formats/CMakeFiles/pdbqtformat.dir/pdbqtformat.o.d -o 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 _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations] > 2871 | const std::binder1st<std::equal_to<OBStereo::Ref> > equal_to_atomId = std::bind1st (equal_to<OBStereo::Ref>(), 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 _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations] > 2903 | const std::binder1st<std::equal_to<OBStereo::Ref> > equal_to_implicitRef = std::bind1st (equal_to<OBStereo::Ref>(), (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 -Dabinitformat_EXPORTS -Iinclude 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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 <min> value or use a ...<max> 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 <min> value or use a ...<max> 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' >
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