* Package: sci-biology/kallisto-0.46.1  * Repository: gentoo  * Maintainer: sci-biology@gentoo.org  * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU  * FEATURES: network-sandbox nostrip preserve-libs sandbox splitdebug userpriv usersandbox >>> Unpacking source... >>> Unpacking kallisto-0.46.1.tar.gz to /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work >>> Source unpacked in /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work >>> Preparing source in /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 ... * Hardcoded definition(s) removed in CMakeLists.txt: * set(CMAKE_BUILD_TYPE "Release") >>> Source prepared. >>> Configuring source in /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 ... >>> Working in BUILD_DIR: "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build" cmake -C /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/gentoo_toolchain.cmake /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 loading initial cache file /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_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 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 -O2 -pipe -march=native -ftree-vectorize C++ -O2 -pipe -march=native -ftree-vectorize Linker flags: Executable -Wl,-O1 -Wl,--as-needed Module -Wl,-O1 -Wl,--as-needed Shared -Wl,-O1 -Wl,--as-needed -- Configuring done -- Generating done -- Build files have been written to: /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build >>> Source configured. >>> Compiling source in /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 ... >>> Working in BUILD_DIR: "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build" make -j1 VERBOSE=1 /usr/bin/cmake -S/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 -B/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build' make -f CMakeFiles/htslib.dir/build.make CMakeFiles/htslib.dir/depend make[2]: Entering directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build' cd /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles/htslib.dir/DependInfo.cmake --color= Dependee "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles/htslib.dir/DependInfo.cmake" is newer than depender "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles/htslib.dir/depend.internal". Dependee "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles/htslib.dir/depend.internal". Scanning dependencies of target htslib make[2]: Leaving directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build' make -f CMakeFiles/htslib.dir/build.make CMakeFiles/htslib.dir/build make[2]: Entering directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build' [ 3%] Creating directories for 'htslib' /usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib /usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib /usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib /usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/tmp /usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp /usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src /usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp /usr/bin/cmake -E touch /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-mkdir [ 6%] No download step for 'htslib' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-download [ 10%] No update step for 'htslib' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-update [ 13%] No patch step for 'htslib' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-patch [ 17%] Performing configure step for 'htslib' cd /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib && autoheader && autoconf && /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/configure --prefix= --disable-bz2 --disable-lzma --disable-libcurl configure.ac:26: warning: AC_INIT: not a literal: make3: Entering directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib' configure.ac:26: 1.4.1 configure.ac:26: make3: Leaving directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib' configure.ac:26: warning: AC_INIT: not a literal: make3: Entering directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib' configure.ac:26: 1.4.1 configure.ac:26: make3: Leaving directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib' /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/configure: line 4: 1.4.1: command not found /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/configure: line 5: make3:: command not found checking for gcc... gcc checking whether the C compiler works... no configure: error: in `/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib': configure: error: C compiler cannot create executables See `config.log' for more details make[2]: *** [CMakeFiles/htslib.dir/build.make:127: /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-configure] Error 77 make[2]: Leaving directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build' make[1]: *** [CMakeFiles/Makefile2:117: CMakeFiles/htslib.dir/all] Error 2 make[1]: Leaving directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build' make: *** [Makefile:149: all] Error 2 * ERROR: sci-biology/kallisto-0.46.1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/kallisto-0.46.1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/kallisto-0.46.1::gentoo'`. * The complete build log is located at '/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/temp/build.log'. * The ebuild environment file is located at '/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/temp/environment'. * Working directory: '/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build' * S: '/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1'