sci-biology:kallisto-0.46.2:20211226-211928.log

sci-biology:kallisto-0.46.2:20211226-211928.log (text/plain), 13.33 KB, created by Toralf Förster on 2021-12-27 09:02:51 UTC

 * Package:    sci-biology/kallisto-0.46.2
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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
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[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 /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/PseudoBam.cpp
[4/21] /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/common.cpp.o -MF src/CMakeFiles/kallisto_core.dir/common.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/common.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/common.cpp
[5/21] /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/h5utils.cpp.o -MF src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o -c /var/tmp/portage/sci-biology/kallisto-0.46.2/work/kallisto-0.46.2/src/h5utils.cpp
[6/21] /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/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
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[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<int>& fld, const std::vector<int>& preBias, const std::vector<double>& 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'