* Package: sci-biology/kallisto-0.46.2 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_musl kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking kallisto-0.46.2.tar.gz to /var/tmp/portage/sci-biology/kallisto-0.46.2/work >>> Source unpacked in /var/tmp/portage/sci-biology/kallisto-0.46.2/work >>> Preparing source in /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2 ... * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2" * Build directory (BUILD_DIR): "/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2_build" * Applying kallisto-0.46.2-cmake.patch ... [ ok ] * Applying kallisto-0.46.2-htslib.patch ... [ ok ] * Applying kallisto-0.46.2-catch2.patch ... [ ok ] * Applying kallisto-0.46.2-gcc11.patch ... [ ok ] * Hardcoded definition(s) removed in CMakeLists.txt: * set(CMAKE_BUILD_TYPE "Release") >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2 ... * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2" * Build directory (BUILD_DIR): "/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2_build" cmake -C /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DUSE_HDF5=no -DBUILD_TESTING=no -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2_build/gentoo_toolchain.cmake /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2 loading initial cache file /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2_build/gentoo_common_config.cmake -- The C compiler identification is GNU 11.2.1 -- The CXX compiler identification is GNU 11.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-gentoo-linux-musl-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-gentoo-linux-musl-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/x86_64-gentoo-linux-musl-pkg-config (found version "1.8.0") -- Checking for module 'htslib' -- Found htslib, version 1.13 -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -pipe -march=native -fno-diagnostics-color -O2 C++ -pipe -march=native -fno-diagnostics-color -O2 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-0.46.2/work/kallisto-0.46.2_build >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2 ... * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2" * Build directory (BUILD_DIR): "/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2_build" ninja -v -j4 -l0 [1/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/hash.cpp.o -MF src/CMakeFiles/kallisto_core.dir/hash.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/hash.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/hash.cpp [2/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/weights.cpp.o -MF src/CMakeFiles/kallisto_core.dir/weights.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/weights.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/weights.cpp [3/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -MF src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c 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-I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -MF src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/KmerIterator.cpp [7/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/main.cpp.o -MF src/CMakeFiles/kallisto_core.dir/main.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/main.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/main.cpp [8/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -MF src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/ProcessReads.cpp [9/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -MF src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/PlaintextWriter.cpp [10/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -MF src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/H5Writer.cpp [11/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -MF src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/MinCollector.cpp [12/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o -MF src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/Kmer.cpp [13/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -MF src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/BUSTools.cpp [14/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto.dir/main.cpp.o -MF src/CMakeFiles/kallisto.dir/main.cpp.o.d -o src/CMakeFiles/kallisto.dir/main.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/main.cpp [15/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -MF src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/Bootstrap.cpp FAILED: src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -MF src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/Bootstrap.cpp In file included from /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/Bootstrap.cpp:1: /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/Bootstrap.h:57:106: error: 'uint' has not been declared 57 | const std::vector& fld, const std::vector& preBias, const std::vector& postBias, uint compression, size_t index_version, | ^~~~ [16/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/Merge.cpp.o -MF src/CMakeFiles/kallisto_core.dir/Merge.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/Merge.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/Merge.cpp [17/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -MF src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/GeneModel.cpp [18/21] /usr/bin/x86_64-gentoo-linux-musl-g++ -I/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src -pipe -march=native -fno-diagnostics-color -O2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -MF src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/KmerIndex.cpp ninja: build stopped: subcommand failed. * ERROR: sci-biology/kallisto-0.46.2::gentoo failed (compile phase): * ninja -v -j4 -l0 failed * * Call stack: * ebuild.sh, line 127: Called src_compile * environment, line 2096: Called cmake_src_compile * environment, line 813: Called cmake_build * environment, line 782: Called eninja * environment, line 1265: Called die * The specific snippet of code: * "$@" || die "${nonfatal_args[@]}" "${*} failed" * * If you need support, post the output of `emerge --info '=sci-biology/kallisto-0.46.2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/kallisto-0.46.2::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:kallisto-0.46.2:20211226-211928.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/kallisto-0.46.2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/kallisto-0.46.2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2_build' * S: '/var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2'