* Package: sci-biology/kallisto-0.43.1 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox splitdebug userpriv usersandbox >>> Unpacking source... >>> Unpacking kallisto-0.43.1.tar.gz to /var/tmp/portage/sci-biology/kallisto-0.43.1/work >>> Source unpacked in /var/tmp/portage/sci-biology/kallisto-0.43.1/work >>> Preparing source in /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build" cmake -C /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/gentoo_toolchain.cmake /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1 loading initial cache file /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/gentoo_common_config.cmake -- The C compiler identification is GNU 11.1.0 -- The CXX compiler identification is GNU 11.1.0 -- 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 shared build -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found HDF5: /usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.10.5") -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -pipe -march=native -fno-diagnostics-color -Og -g C++ -pipe -march=native -fno-diagnostics-color -Og -g Linker flags: Executable -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Module -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Shared -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-biology/kallisto-0.43.1/work/kallisto-0.43.1_build >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build" make -j 1 VERBOSE=1 /usr/bin/cmake -S/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1 -B/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/CMakeFiles /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build' cd /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1 /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/src /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake make[2]: Leaving directory '/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build make[2]: Entering directory '/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build' [ 5%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o cd /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/../ext -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src -DNDEBUG -pipe -march=native -fno-diagnostics-color -Og -g -std=c++11 -O3 -MD -MT src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -MF CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o.d -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/Bootstrap.cpp [ 11%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o cd /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/../ext -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src -DNDEBUG -pipe -march=native -fno-diagnostics-color -Og -g -std=c++11 -O3 -MD -MT src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -MF CMakeFiles/kallisto_core.dir/H5Writer.cpp.o.d -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/H5Writer.cpp [ 17%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o cd /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/../ext -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src -DNDEBUG -pipe -march=native -fno-diagnostics-color -Og -g -std=c++11 -O3 -MD -MT src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o -MF CMakeFiles/kallisto_core.dir/Kmer.cpp.o.d -o CMakeFiles/kallisto_core.dir/Kmer.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/Kmer.cpp [ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o cd /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/../ext -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src -DNDEBUG -pipe -march=native -fno-diagnostics-color -Og -g -std=c++11 -O3 -MD -MT src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -MF CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o.d -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/KmerIndex.cpp [ 29%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o cd /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/../ext -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src -DNDEBUG -pipe -march=native -fno-diagnostics-color -Og -g -std=c++11 -O3 -MD -MT src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -MF CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o.d -o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/KmerIterator.cpp [ 35%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o cd /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/../ext -I/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src -DNDEBUG -pipe -march=native -fno-diagnostics-color -Og -g -std=c++11 -O3 -MD -MT src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -MF CMakeFiles/kallisto_core.dir/MinCollector.cpp.o.d -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/MinCollector.cpp /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/MinCollector.cpp: In member function ‘std::vector MinCollector::intersectECs(std::vector >&) const’: /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/MinCollector.cpp:194:21: error: ‘numeric_limits’ is not a member of ‘std’ 194 | int minpos = std::numeric_limits::max(); | ^~~~~~~~~~~~~~ /var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1/src/MinCollector.cpp:194:36: error: expected primary-expression before ‘int’ 194 | int minpos = std::numeric_limits::max(); | ^~~ make[2]: *** [src/CMakeFiles/kallisto_core.dir/build.make:146: src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build' make[1]: *** [CMakeFiles/Makefile2:126: src/CMakeFiles/kallisto_core.dir/all] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build' make: *** [Makefile:136: all] Error 2 * ERROR: sci-biology/kallisto-0.43.1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/kallisto-0.43.1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/kallisto-0.43.1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:kallisto-0.43.1:20210505-190312.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/kallisto-0.43.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/kallisto-0.43.1/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1_build' * S: '/var/tmp/portage/sci-biology/kallisto-0.43.1/work/kallisto-0.43.1'