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Gentoo's Bugzilla – Attachment 893312 Details for
Bug 932158
sci-libs/libcifpp-7.0.4 - sandbox issue
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sci-libs:libcifpp-7.0.4:20240518-134318.log
sci-libs:libcifpp-7.0.4:20240518-134318.log (text/plain), 26.01 KB, created by
Toralf Förster
on 2024-05-18 14:05:50 UTC
(
hide
)
Description:
sci-libs:libcifpp-7.0.4:20240518-134318.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2024-05-18 14:05:50 UTC
Size:
26.01 KB
patch
obsolete
> * Package: sci-libs/libcifpp-7.0.4:0 > * Repository: gentoo > * Maintainer: pacho@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox > >>>> Unpacking source... >>>> Unpacking libcifpp-7.0.4.tar.gz to /var/tmp/portage/sci-libs/libcifpp-7.0.4/work >>>> Unpacking libcifpp-7.0.4-components.cif.xz to /var/tmp/portage/sci-libs/libcifpp-7.0.4/work >>>> Source unpacked in /var/tmp/portage/sci-libs/libcifpp-7.0.4/work >>>> Preparing source in /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4 ... > * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4" > * Build directory (BUILD_DIR): "/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4_build" > * Hardcoded definition(s) removed in CMakeLists.txt: > * set(CMAKE_INSTALL_PREFIX "$ENV{CCP4}") >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4 ... > * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4" > * Build directory (BUILD_DIR): "/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4_build" >cmake -C /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_SHARED_LIBS=ON -DCIFPP_INSTALL_UPDATE_SCRIPT=OFF -DBUILD_TESTING=no -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4_build/gentoo_toolchain.cmake /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4 >loading initial cache file /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4_build/gentoo_common_config.cmake >-- The CXX compiler identification is GNU 13.2.1 >-- 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 >-- DESTDIR is '' >-- Performing Test GXX_LIBSTDCPP >-- Performing Test GXX_LIBSTDCPP - Success >-- Testing for known regex bug, since you're using GNU libstdc++ >-- You are probably trying to compile using the g++ standard library which contains a crashing std::regex implementation. Will use boost::regex instead >-- Performing Test CMAKE_HAVE_LIBC_PTHREAD >-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success >-- Found Threads: TRUE >-- Git hash not found >-- 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 >-- Installation will remove old config files: /usr/lib64/cmake/cifpp/cifppConfig.cmake;/usr/lib64/cmake/cifpp/cifppConfigVersion.cmake;/usr/lib64/cmake/cifpp/cifppTargets-relwithdebinfo.cmake;/usr/lib64/cmake/cifpp/cifppTargets.cmake >-- <<< Gentoo configuration >>> >Build type RelWithDebInfo >Install path /usr >Compiler flags: >C >C++ -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers >Linker flags: >Executable -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0 >Module -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0 >Shared -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0 > >-- Configuring done (11.5s) >-- Generating done (0.0s) >-- Build files have been written to: /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4_build >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4 ... > * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4" > * Build directory (BUILD_DIR): "/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4_build" >ninja -v -j4 -l0 >[1/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/condition.cpp.o -MF CMakeFiles/cifpp.dir/src/condition.cpp.o.d -o CMakeFiles/cifpp.dir/src/condition.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/condition.cpp >[2/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/datablock.cpp.o -MF CMakeFiles/cifpp.dir/src/datablock.cpp.o.d -o CMakeFiles/cifpp.dir/src/datablock.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/datablock.cpp >[3/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/item.cpp.o -MF CMakeFiles/cifpp.dir/src/item.cpp.o.d -o CMakeFiles/cifpp.dir/src/item.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/item.cpp >[4/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/file.cpp.o -MF CMakeFiles/cifpp.dir/src/file.cpp.o.d -o CMakeFiles/cifpp.dir/src/file.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/file.cpp >[5/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/dictionary_parser.cpp.o -MF CMakeFiles/cifpp.dir/src/dictionary_parser.cpp.o.d -o CMakeFiles/cifpp.dir/src/dictionary_parser.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/dictionary_parser.cpp >[6/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/row.cpp.o -MF CMakeFiles/cifpp.dir/src/row.cpp.o.d -o CMakeFiles/cifpp.dir/src/row.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/row.cpp >[7/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/category.cpp.o -MF CMakeFiles/cifpp.dir/src/category.cpp.o.d -o CMakeFiles/cifpp.dir/src/category.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/category.cpp >[8/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/parser.cpp.o -MF CMakeFiles/cifpp.dir/src/parser.cpp.o.d -o CMakeFiles/cifpp.dir/src/parser.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/parser.cpp >[9/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/text.cpp.o -MF CMakeFiles/cifpp.dir/src/text.cpp.o.d -o CMakeFiles/cifpp.dir/src/text.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/text.cpp >[10/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/atom_type.cpp.o -MF CMakeFiles/cifpp.dir/src/atom_type.cpp.o.d -o CMakeFiles/cifpp.dir/src/atom_type.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/atom_type.cpp >[11/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/utilities.cpp.o -MF CMakeFiles/cifpp.dir/src/utilities.cpp.o.d -o CMakeFiles/cifpp.dir/src/utilities.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/utilities.cpp >[12/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/point.cpp.o -MF CMakeFiles/cifpp.dir/src/point.cpp.o.d -o CMakeFiles/cifpp.dir/src/point.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/point.cpp >[13/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/validate.cpp.o -MF CMakeFiles/cifpp.dir/src/validate.cpp.o.d -o CMakeFiles/cifpp.dir/src/validate.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/validate.cpp >[14/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/compound.cpp.o -MF CMakeFiles/cifpp.dir/src/compound.cpp.o.d -o CMakeFiles/cifpp.dir/src/compound.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/compound.cpp >[15/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/model.cpp.o -MF CMakeFiles/cifpp.dir/src/model.cpp.o.d -o CMakeFiles/cifpp.dir/src/model.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/model.cpp >[16/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/symmetry.cpp.o -MF CMakeFiles/cifpp.dir/src/symmetry.cpp.o.d -o CMakeFiles/cifpp.dir/src/symmetry.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/symmetry.cpp >[17/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/pdb/pdb2cif_remark_3.cpp.o -MF CMakeFiles/cifpp.dir/src/pdb/pdb2cif_remark_3.cpp.o.d -o CMakeFiles/cifpp.dir/src/pdb/pdb2cif_remark_3.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/pdb/pdb2cif_remark_3.cpp >[18/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/pdb/reconstruct.cpp.o -MF CMakeFiles/cifpp.dir/src/pdb/reconstruct.cpp.o.d -o CMakeFiles/cifpp.dir/src/pdb/reconstruct.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/pdb/reconstruct.cpp >In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/string:42, > from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/stdexcept:39, > from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/system_error:43, > from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/bits/fs_fwd.h:35, > from /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/filesystem:48, > from /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include/cif++/utilities.hpp:31, > from /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include/cif++.hpp:29, > from /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/pdb/reconstruct.cpp:27: >In static member function âstatic constexpr void std::char_traits<char>::assign(char_type&, const char_type&)â, > inlined from âconstexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::push_back(_CharT) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/bits/basic_string.h:1566:21, > inlined from âconstexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator+=(_CharT) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/bits/basic_string.h:1388:17, > inlined from âvoid cif::pdb::createEntityPoly(cif::datablock&)â at /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/pdb/reconstruct.cpp:822:29: >/usr/lib/gcc/x86_64-pc-linux-gnu/13/include/g++-v13/bits/char_traits.h:358:14: warning: âletter_canâ may be used uninitialized [-Wmaybe-uninitialized] > 358 | __c1 = __c2; > | ~~~~~^~~~~~ >/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/pdb/reconstruct.cpp: In function âvoid cif::pdb::createEntityPoly(cif::datablock&)â: >/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/pdb/reconstruct.cpp:769:30: note: âletter_canâ was declared here > 769 | char letter_can; > | ^~~~~~~~~~ >[19/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/pdb/validate-pdbx.cpp.o -MF CMakeFiles/cifpp.dir/src/pdb/validate-pdbx.cpp.o.d -o CMakeFiles/cifpp.dir/src/pdb/validate-pdbx.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/pdb/validate-pdbx.cpp >[20/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/pdb/cif2pdb.cpp.o -MF CMakeFiles/cifpp.dir/src/pdb/cif2pdb.cpp.o.d -o CMakeFiles/cifpp.dir/src/pdb/cif2pdb.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/pdb/cif2pdb.cpp >[21/22] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_REGEX_STANDALONE=1 -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -DUSE_BOOST_REGEX=1 -I/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/include -I/usr/include/eigen3 -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/cifpp.dir/src/pdb/pdb2cif.cpp.o -MF CMakeFiles/cifpp.dir/src/pdb/pdb2cif.cpp.o.d -o CMakeFiles/cifpp.dir/src/pdb/pdb2cif.cpp.o -c /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4/src/pdb/pdb2cif.cpp >[22/22] : && /usr/bin/cmake -E rm -f libcifpp.a && /usr/bin/x86_64-pc-linux-gnu-ar qc libcifpp.a CMakeFiles/cifpp.dir/src/category.cpp.o CMakeFiles/cifpp.dir/src/condition.cpp.o CMakeFiles/cifpp.dir/src/datablock.cpp.o CMakeFiles/cifpp.dir/src/dictionary_parser.cpp.o CMakeFiles/cifpp.dir/src/file.cpp.o CMakeFiles/cifpp.dir/src/item.cpp.o CMakeFiles/cifpp.dir/src/parser.cpp.o CMakeFiles/cifpp.dir/src/row.cpp.o CMakeFiles/cifpp.dir/src/validate.cpp.o CMakeFiles/cifpp.dir/src/text.cpp.o CMakeFiles/cifpp.dir/src/utilities.cpp.o CMakeFiles/cifpp.dir/src/atom_type.cpp.o CMakeFiles/cifpp.dir/src/compound.cpp.o CMakeFiles/cifpp.dir/src/point.cpp.o CMakeFiles/cifpp.dir/src/symmetry.cpp.o CMakeFiles/cifpp.dir/src/model.cpp.o CMakeFiles/cifpp.dir/src/pdb/cif2pdb.cpp.o CMakeFiles/cifpp.dir/src/pdb/pdb2cif.cpp.o CMakeFiles/cifpp.dir/src/pdb/pdb2cif_remark_3.cpp.o CMakeFiles/cifpp.dir/src/pdb/reconstruct.cpp.o CMakeFiles/cifpp.dir/src/pdb/validate-pdbx.cpp.o && /usr/bin/x86_64-pc-linux-gnu-ranlib libcifpp.a && : >>>> Source compiled. > * Skipping make test/check due to ebuild restriction. >>>> Test phase [disabled because of RESTRICT=test]: sci-libs/libcifpp-7.0.4 > >>>> Install sci-libs/libcifpp-7.0.4 into /var/tmp/portage/sci-libs/libcifpp-7.0.4/image > * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4" > * Build directory (BUILD_DIR): "/var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4_build" >ninja -v -j4 -l0 install >[0/1] cd /var/tmp/portage/sci-libs/libcifpp-7.0.4/work/libcifpp-7.0.4_build && /usr/bin/cmake -P cmake_install.cmake >-- Install configuration: "RelWithDebInfo" >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/lib64/libcifpp.a >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/atom_type.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/category.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/compound.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/condition.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/datablock.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/dictionary_parser.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/exports.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/file.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/format.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/forward_decl.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/gzio.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/item.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/iterator.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/matrix.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/model.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/parser.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/pdb.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/point.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/row.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/symmetry.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/text.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/utilities.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/validate.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/pdb/cif2pdb.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/pdb/io.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/pdb/pdb2cif.hpp >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/include/cif++/pdb/tls.hpp > * ACCESS DENIED: unlink: /usr/lib64/cmake/cifpp/cifppConfig.cmake > * ACCESS DENIED: unlink: /usr/lib64/cmake/cifpp/cifppConfigVersion.cmake > * ACCESS DENIED: unlink: /usr/lib64/cmake/cifpp/cifppTargets-relwithdebinfo.cmake > * ACCESS DENIED: unlink: /usr/lib64/cmake/cifpp/cifppTargets.cmake >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/lib/cmake/cifpp/cifpp-targets.cmake >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/lib/cmake/cifpp/cifpp-targets-relwithdebinfo.cmake >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/share/libcifpp/mmcif_ddl.dic >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/share/libcifpp/mmcif_pdbx.dic >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/share/libcifpp/mmcif_ma.dic >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/share/libcifpp/components.cif >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/lib/cmake/cifpp/cifpp-config.cmake >-- Installing: /var/tmp/portage/sci-libs/libcifpp-7.0.4/image/usr/lib/cmake/cifpp/cifpp-config-version.cmake >>>> Completed installing sci-libs/libcifpp-7.0.4 into /var/tmp/portage/sci-libs/libcifpp-7.0.4/image > > * Final size of build directory: 861068 KiB (840.8 MiB) > * Final size of installed tree: 433932 KiB (423.7 MiB) > > * ----------------------- SANDBOX ACCESS VIOLATION SUMMARY ----------------------- > * LOG FILE: "/var/tmp/portage/sci-libs/libcifpp-7.0.4/temp/sandbox.log" > * >VERSION 1.0 >FORMAT: F - Function called >FORMAT: S - Access Status >FORMAT: P - Path as passed to function >FORMAT: A - Absolute Path (not canonical) >FORMAT: R - Canonical Path >FORMAT: C - Command Line > >F: unlink >S: deny >P: /usr/lib64/cmake/cifpp/cifppConfig.cmake >A: /usr/lib64/cmake/cifpp/cifppConfig.cmake >R: /usr/lib64/cmake/cifpp/cifppConfig.cmake >C: /usr/bin/cmake -P cmake_install.cmake > >F: unlink >S: deny >P: /usr/lib64/cmake/cifpp/cifppConfigVersion.cmake >A: /usr/lib64/cmake/cifpp/cifppConfigVersion.cmake >R: /usr/lib64/cmake/cifpp/cifppConfigVersion.cmake >C: /usr/bin/cmake -P cmake_install.cmake > >F: unlink >S: deny >P: /usr/lib64/cmake/cifpp/cifppTargets-relwithdebinfo.cmake >A: /usr/lib64/cmake/cifpp/cifppTargets-relwithdebinfo.cmake >R: /usr/lib64/cmake/cifpp/cifppTargets-relwithdebinfo.cmake >C: /usr/bin/cmake -P cmake_install.cmake > >F: unlink >S: deny >P: /usr/lib64/cmake/cifpp/cifppTargets.cmake >A: /usr/lib64/cmake/cifpp/cifppTargets.cmake >R: /usr/lib64/cmake/cifpp/cifppTargets.cmake >C: /usr/bin/cmake -P cmake_install.cmake > * -------------------------------------------------------------------------------- >
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