sci-biology:somatic-sniper-1.0.4:20201119-094112.log

sci-biology:somatic-sniper-1.0.4:20201119-094112.log (text/plain), 10.97 KB, created by Toralf Förster on 2020-11-19 13:10:42 UTC

 * Package:    sci-biology/somatic-sniper-1.0.4
 * Repository: science
 * Maintainer: [e-mail] [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking somatic-sniper-1.0.4.tar.gz to /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work
>>> Source unpacked in /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work
>>> Preparing source in /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4 ...
 * Hardcoded definition(s) removed in CMakeLists.txt:
 *  set(CMAKE_INSTALL_PREFIX "/usr")
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build"
cmake --no-warn-unused-cli -C /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/gentoo_toolchain.cmake  /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4
Not searching for unused variables given on the command line.
loading initial cache file /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/gentoo_common_config.cmake
-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- 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
-- 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 ZLIB: /usr/lib64/libz.so (found version "1.2.11") 
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -Wall
C++             -Wall -ansi -pedantic -Wno-long-long -Wno-variadic-macros
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/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build"
make -j1 VERBOSE=1 
/usr/bin/cmake -S/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4 -B/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/CMakeFiles /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build//CMakeFiles/progress.marks
make  -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build'
make  -f CMakeFiles/samtools-lib.dir/build.make CMakeFiles/samtools-lib.dir/depend
make[2]: Entering directory '/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build'
cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4 /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4 /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/CMakeFiles/samtools-lib.dir/DependInfo.cmake
Dependee "/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/CMakeFiles/samtools-lib.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/CMakeFiles/samtools-lib.dir/depend.internal".
Dependee "/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/CMakeFiles/samtools-lib.dir/depend.internal".
Scanning dependencies of target samtools-lib
make[2]: Leaving directory '/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build'
make  -f CMakeFiles/samtools-lib.dir/build.make CMakeFiles/samtools-lib.dir/build
make[2]: Entering directory '/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build'
[  3%] Creating directories for 'samtools-lib'
/usr/bin/cmake -E make_directory /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/samtools
/usr/bin/cmake -E make_directory /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/samtools
/usr/bin/cmake -E make_directory /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor
/usr/bin/cmake -E make_directory /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/tmp
/usr/bin/cmake -E make_directory /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/src/samtools-lib-stamp
/usr/bin/cmake -E make_directory /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/src
/usr/bin/cmake -E make_directory /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/src/samtools-lib-stamp
/usr/bin/cmake -E touch /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/src/samtools-lib-stamp/samtools-lib-mkdir
[  6%] Performing download step (verify and extract) for 'samtools-lib'
cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor && /usr/bin/cmake -P /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/src/samtools-lib-stamp/verify-samtools-lib.cmake
CMake Warning at src/samtools-lib-stamp/verify-samtools-lib.cmake:15 (message):
  File will not be verified since no URL_HASH specified


cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor && /usr/bin/cmake -P /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/src/samtools-lib-stamp/extract-samtools-lib.cmake
-- extracting...
     src='/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4/vendor/samtools-0.1.6.tar.gz'
     dst='/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/samtools'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor && /usr/bin/cmake -E touch /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/src/samtools-lib-stamp/samtools-lib-download
[  9%] No update step for 'samtools-lib'
/usr/bin/cmake -E echo_append
/usr/bin/cmake -E touch /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/src/samtools-lib-stamp/samtools-lib-update
[ 12%] Performing patch step for 'samtools-lib'
cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/samtools && patch -Np1 < /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4/vendor/samtools.patch
patching file Makefile
cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/samtools && /usr/bin/cmake -E touch /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/src/samtools-lib-stamp/samtools-lib-patch
[ 15%] Performing configure step for 'samtools-lib'
cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/samtools && echo "Building samtools, build log at /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/samtools/build.log"
Building samtools, build log at /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/samtools/build.log
cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/samtools && /usr/bin/cmake -E touch /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/src/samtools-lib-stamp/samtools-lib-configure
[ 18%] Performing build step for 'samtools-lib'
cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/samtools && make > /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/vendor/samtools/build.log 2>&1
make[2]: *** [CMakeFiles/samtools-lib.dir/build.make:132: vendor/src/samtools-lib-stamp/samtools-lib-build] Error 2
make[2]: Leaving directory '/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build'
make[1]: *** [CMakeFiles/Makefile2:232: CMakeFiles/samtools-lib.dir/all] Error 2
make[1]: Leaving directory '/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build'
make: *** [Makefile:182: all] Error 2
 * ERROR: sci-biology/somatic-sniper-1.0.4::science failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/somatic-sniper-1.0.4::science'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/somatic-sniper-1.0.4::science'`.
 * The complete build log is located at '/var/log/portage/sci-biology:somatic-sniper-1.0.4:20201119-094112.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build'
 * S: '/var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4'