sci-biology:kallisto-0.43.1:20210505-190312.log

sci-biology:kallisto-0.43.1:20210505-190312.log (text/plain), 10.49 KB, created by Toralf Förster on 2021-05-05 20:19:17 UTC

 * Package:    sci-biology/kallisto-0.43.1
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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<int> MinCollector::intersectECs(std::vector<std::pair<KmerEntry, int> >&) 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<int>::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<int>::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'