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spades (homebrew/science/spades) on "Red Hat Enterprise Linux Server release 7.2 (Maipo)" - Homebrew build logs
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| Homebrew build logs for homebrew/science/spades on "Red Hat Enterprise Linux Server release 7.2 (Maipo)" | |
| Build date: 2016-06-01 10:56:34 |
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| HOMEBREW_VERSION: 0.9.9 | |
| ORIGIN: https://github.com/Linuxbrew/brew.git | |
| HEAD: 68c10e47400571d20c1c6dc407a7d9b7c32ba79a | |
| Last commit: 4 days ago | |
| Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core | |
| Core tap HEAD: 91737fc35c3023ef52d9696505e41639c59072a1 | |
| Core tap last commit: 39 minutes ago | |
| HOMEBREW_PREFIX: /bio/linuxbrew | |
| HOMEBREW_REPOSITORY: /bio/linuxbrew | |
| HOMEBREW_CELLAR: /bio/linuxbrew/Cellar | |
| HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com | |
| CPU: 72-core 64-bit haswell | |
| Kernel: Linux 3.10.0-327.18.2.el7.x86_64 x86_64 GNU/Linux | |
| OS: Red Hat Enterprise Linux Server release 7.2 (Maipo) | |
| Codename: Maipo | |
| OS glibc: 2.17 | |
| OS gcc: 4.8.5 | |
| Linuxbrew glibc: N/A | |
| Linuxbrew gcc: 5.3.0 | |
| Clang: N/A | |
| X11: N/A | |
| System Ruby: 2.3.0 => /bio/linuxbrew/Cellar/ruby/2.3.0/bin/ruby | |
| Perl: /usr/bin/perl | |
| Python: /bio/linuxbrew/bin/python => /bio/linuxbrew/Cellar/python/2.7.11/bin/python2.7 | |
| Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.3.0/bin/ruby | |
| Java: openjdk version "1.8.0_91" |
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| Please note that these warnings are just used to help the Homebrew maintainers | |
| with debugging if you file an issue. If everything you use Homebrew for is | |
| working fine: please don't worry and just ignore them. Thanks! | |
| Warning: You have unlinked kegs in your Cellar | |
| Leaving kegs unlinked can lead to build-trouble and cause brews that depend on | |
| those kegs to fail to run properly once built. Run `brew link` on these: | |
| minia | |
| viennarna | |
| barrnap | |
| libdivsufsort | |
| snippy | |
| prokka | |
| mlst | |
| abricate | |
| nullarbor | |
| tmux | |
| Warning: Broken symlinks were found. Remove them with `brew prune`: | |
| /bio/linuxbrew/lib/R/library/survival/NEWS.Rd.orig |
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| Formula: spades | |
| Tap: homebrew/science | |
| Path: /bio/linuxbrew/Library/Taps/homebrew/homebrew-science/spades.rb |
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| 2016-06-01 10:56:20 +1000 | |
| cmake | |
| .. | |
| -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG | |
| -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG | |
| -DCMAKE_INSTALL_PREFIX=/bio/linuxbrew/Cellar/spades/3.8.0 | |
| -DCMAKE_BUILD_TYPE=Release | |
| -DCMAKE_FIND_FRAMEWORK=LAST | |
| -DCMAKE_VERBOSE_MAKEFILE=ON | |
| -Wno-dev | |
| -DCMAKE_BUILD_WITH_INSTALL_RPATH=1 | |
| -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=1 | |
| -- The C compiler identification is GNU 5.3.0 | |
| -- The CXX compiler identification is GNU 5.3.0 | |
| -- Check for working C compiler: /bio/linuxbrew/bin/gcc-5 | |
| -- Check for working C compiler: /bio/linuxbrew/bin/gcc-5 -- works | |
| -- Detecting C compiler ABI info | |
| -- Detecting C compiler ABI info - done | |
| -- Detecting C compile features | |
| -- Detecting C compile features - done | |
| -- Check for working CXX compiler: /bio/linuxbrew/bin/g++-5 | |
| -- Check for working CXX compiler: /bio/linuxbrew/bin/g++-5 -- works | |
| -- Detecting CXX compiler ABI info | |
| -- Detecting CXX compiler ABI info - done | |
| -- Detecting CXX compile features | |
| -- Detecting CXX compile features - done | |
| -- Try OpenMP C flag = [-fopenmp] | |
| -- Performing Test OpenMP_FLAG_DETECTED | |
| -- Performing Test OpenMP_FLAG_DETECTED - Success | |
| -- Try OpenMP CXX flag = [-fopenmp] | |
| -- Performing Test OpenMP_FLAG_DETECTED | |
| -- Performing Test OpenMP_FLAG_DETECTED - Success | |
| -- Found OpenMP: -fopenmp | |
| -- Found ZLIB: /bio/linuxbrew/lib64/libz.so (found version "1.2.8") | |
| -- Found BZip2: /bio/linuxbrew/lib64/libbz2.so (found version "1.0.6") | |
| -- Looking for BZ2_bzCompressInit | |
| -- Looking for BZ2_bzCompressInit - found | |
| -- Found readline: /bio/linuxbrew/include | |
| -- Looking for wsyncup in /bio/linuxbrew/lib64/libncurses.so | |
| -- Looking for wsyncup in /bio/linuxbrew/lib64/libncurses.so - found | |
| -- Looking for wsyncup in /bio/linuxbrew/lib64/libcurses.so | |
| -- Looking for wsyncup in /bio/linuxbrew/lib64/libcurses.so - found | |
| -- Boost version: 1.60.0 | |
| Making Release Configuration... | |
| Building SPAdes from N/A, sha: N/A | |
| -- Looking for include file features.h | |
| -- Looking for include file features.h - found | |
| -- Looking for include file sys/cdefs.h | |
| -- Looking for include file sys/cdefs.h - found | |
| -- Looking for atomic_fetchadd_long | |
| -- Looking for atomic_fetchadd_long - not found | |
| -- Looking for OSAtomicAdd64 | |
| -- Looking for OSAtomicAdd64 - not found | |
| -- Looking for OSSpinLockLock | |
| -- Looking for OSSpinLockLock - not found | |
| -- Looking for _malloc_thread_cleanup | |
| -- Looking for _malloc_thread_cleanup - not found | |
| -- Looking for _pthread_mutex_init_calloc_cb, | |
| -- Looking for _pthread_mutex_init_calloc_cb, - not found | |
| -- Looking for sbrk | |
| -- Looking for sbrk - found | |
| -- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED | |
| -- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED - Success | |
| -- Looking for sys/types.h | |
| -- Looking for sys/types.h - found | |
| -- Looking for stdint.h | |
| -- Looking for stdint.h - found | |
| -- Looking for stddef.h | |
| -- Looking for stddef.h - found | |
| -- Check size of void* | |
| -- Check size of void* - done | |
| -- Performing Test JEMALLOC_TLS | |
| -- Performing Test JEMALLOC_TLS - Success | |
| -- Looking for memalign | |
| -- Looking for memalign - found | |
| -- Looking for valloc | |
| -- Looking for valloc - found | |
| -- Check size of int | |
| -- Check size of int - done | |
| -- Check size of long | |
| -- Check size of long - done | |
| -- Check size of intmax_t | |
| -- Check size of intmax_t - done | |
| -- Looking for open | |
| -- Looking for open - found | |
| -- Looking for include file execinfo.h | |
| -- Looking for include file execinfo.h - found | |
| -- Looking for include file signal.h | |
| -- Looking for include file signal.h - found | |
| -- Looking for include file sys/stat.h | |
| -- Looking for include file sys/stat.h - found | |
| -- Looking for include file cxxabi.h | |
| -- Looking for include file cxxabi.h - not found | |
| -- Looking for include file dlfcn.h | |
| -- Looking for include file dlfcn.h - found | |
| -- Looking for include file mach/mach.h | |
| -- Looking for include file mach/mach.h - not found | |
| -- Looking for include file link.h | |
| -- Looking for include file link.h - found | |
| -- Looking for backtrace | |
| -- Looking for backtrace - found | |
| -- Looking for pthread.h | |
| -- Looking for pthread.h - found | |
| -- Looking for pthread_create | |
| -- Looking for pthread_create - found | |
| -- Found Threads: TRUE | |
| -- Looking for shm_open | |
| -- Looking for shm_open - not found | |
| -- Looking for shm_open in rt | |
| -- Looking for shm_open in rt - found | |
| -- Configuring done | |
| -- Generating done | |
| -- Build files have been written to: /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build |
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| 2016-06-01 10:56:34 +1000 | |
| make | |
| install | |
| /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -H/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -B/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build --check-build-system CMakeFiles/Makefile.cmake 0 | |
| /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_progress_start /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/CMakeFiles /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/CMakeFiles/progress.marks | |
| make -f CMakeFiles/Makefile2 all | |
| make[1]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make -f ext/jemalloc/CMakeFiles/jemalloc.dir/build.make ext/jemalloc/CMakeFiles/jemalloc.dir/depend | |
| make -f ext/nlopt/CMakeFiles/nlopt.dir/build.make ext/nlopt/CMakeFiles/nlopt.dir/depend | |
| make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend | |
| make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend | |
| make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend | |
| make -f ext/ssw/CMakeFiles/ssw.dir/build.make ext/ssw/CMakeFiles/ssw.dir/depend | |
| make -f ext/cityhash/CMakeFiles/cityhash.dir/build.make ext/cityhash/CMakeFiles/cityhash.dir/depend | |
| make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend | |
| make -f ext/htrie/CMakeFiles/hattrie.dir/build.make ext/htrie/CMakeFiles/hattrie.dir/depend | |
| make -f ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/build.make ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/depend | |
| make -f modules/data_structures/sequence/CMakeFiles/sequence.dir/build.make modules/data_structures/sequence/CMakeFiles/sequence.dir/depend | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cityhash /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/cityhash /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/cityhash/CMakeFiles/cityhash.dir/DependInfo.cmake --color= | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake --color= | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc/CMakeFiles/jemalloc.dir/DependInfo.cmake --color= | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt/CMakeFiles/nlopt.dir/DependInfo.cmake --color= | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cppformat /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/cppformat /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake --color= | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ssw /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ssw /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ssw/CMakeFiles/ssw.dir/DependInfo.cmake --color= | |
| make -f modules/algorithms/CMakeFiles/algorithms.dir/build.make modules/algorithms/CMakeFiles/algorithms.dir/depend | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/DependInfo.cmake --color= | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/htrie /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie/CMakeFiles/hattrie.dir/DependInfo.cmake --color= | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/data_structures/sequence /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/data_structures/sequence /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/data_structures/sequence/CMakeFiles/sequence.dir/DependInfo.cmake --color= | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake --color= | |
| make -f modules/stages/CMakeFiles/stages.dir/build.make modules/stages/CMakeFiles/stages.dir/depend | |
| make -f modules/dev_support/CMakeFiles/dev_support.dir/build.make modules/dev_support/CMakeFiles/dev_support.dir/depend | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/algorithms /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/algorithms /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/algorithms/CMakeFiles/algorithms.dir/DependInfo.cmake --color= | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/stages /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/stages /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/stages/CMakeFiles/stages.dir/DependInfo.cmake --color= | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/dev_support /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/dev_support /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/dev_support/CMakeFiles/dev_support.dir/DependInfo.cmake --color= | |
| Scanning dependencies of target hattrie | |
| Scanning dependencies of target ssw | |
| Scanning dependencies of target cityhash | |
| Scanning dependencies of target sequence | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make -f ext/ssw/CMakeFiles/ssw.dir/build.make ext/ssw/CMakeFiles/ssw.dir/build | |
| make -f ext/cityhash/CMakeFiles/cityhash.dir/build.make ext/cityhash/CMakeFiles/cityhash.dir/build | |
| make -f ext/htrie/CMakeFiles/hattrie.dir/build.make ext/htrie/CMakeFiles/hattrie.dir/build | |
| make -f modules/data_structures/sequence/CMakeFiles/sequence.dir/build.make modules/data_structures/sequence/CMakeFiles/sequence.dir/build | |
| Scanning dependencies of target nlopt | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make -f ext/nlopt/CMakeFiles/nlopt.dir/build.make ext/nlopt/CMakeFiles/nlopt.dir/build | |
| [ 1%] Building C object ext/htrie/CMakeFiles/hattrie.dir/ahtable.c.o | |
| [ 3%] Building C object ext/htrie/CMakeFiles/hattrie.dir/murmurhash3.c.o | |
| [ 1%] Building CXX object ext/cityhash/CMakeFiles/cityhash.dir/city.cc.o | |
| [ 0%] Building C object ext/htrie/CMakeFiles/hattrie.dir/hat-trie.c.o | |
| [ 1%] Building CXX object modules/data_structures/sequence/CMakeFiles/sequence.dir/genome_storage.cpp.o | |
| [ 0%] Building CXX object ext/ssw/CMakeFiles/ssw.dir/ssw_cpp.cpp.o | |
| [ 3%] Building C object ext/htrie/CMakeFiles/hattrie.dir/misc.c.o | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 3%] Building C object ext/ssw/CMakeFiles/ssw.dir/ssw.c.o | |
| Scanning dependencies of target format | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ssw && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ssw -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ssw -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/ssw.dir/ssw_cpp.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ssw/ssw_cpp.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/cityhash && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/cityhash -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cityhash -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/cityhash.dir/city.cc.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cityhash/city.cc | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/data_structures/sequence && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/data_structures/sequence -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/data_structures/sequence -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/sequence.dir/genome_storage.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/data_structures/sequence/genome_storage.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/htrie -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/hattrie.dir/ahtable.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/htrie/ahtable.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ssw && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ssw -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ssw -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/ssw.dir/ssw.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ssw/ssw.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/htrie -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/hattrie.dir/hat-trie.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/htrie/hat-trie.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/htrie -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/hattrie.dir/misc.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/htrie/misc.c | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 3%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/api/general.c.o | |
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| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/htrie -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/hattrie.dir/murmurhash3.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/htrie/murmurhash3.c | |
| [ 4%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/bobyqa/bobyqa.c.o | |
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| make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/api/options.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/api/options.c | |
| [ 6%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/cobyla/cobyla.c.o | |
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| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/api/general.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/api/general.c | |
| [ 7%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/mma/ccsa_quadratic.c.o | |
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| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 10%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/util/stop.c.o | |
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| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/api/optimize.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/api/optimize.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/api/deprecated.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/api/deprecated.c | |
| [ 13%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o | |
| [ 13%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/auglag/auglag.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/auglag/auglag.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/bobyqa/bobyqa.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/bobyqa/bobyqa.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/cdirect/cdirect.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/cdirect/cdirect.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/cppformat && /bio/linuxbrew/bin/g++-5 -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/cppformat -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cppformat -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wall -Wextra -pedantic -Wno-deprecated -g0 -O2 -o CMakeFiles/format.dir/format.cc.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cppformat/format.cc | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/cdirect/hybrid.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/cdirect/hybrid.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/cppformat && /bio/linuxbrew/bin/g++-5 -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/cppformat -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cppformat -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wall -Wextra -pedantic -Wno-deprecated -g0 -O2 -o CMakeFiles/format.dir/posix.cc.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cppformat/posix.cc | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/cobyla/cobyla.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/cobyla/cobyla.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/crs/crs.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/crs/crs.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/esch/esch.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/esch/esch.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/isres/isres.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/isres/isres.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/mma/mma.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/mma/mma.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/mma/ccsa_quadratic.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/mma/ccsa_quadratic.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/mlsl/mlsl.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/mlsl/mlsl.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/neldermead/nldrmd.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/neldermead/nldrmd.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/neldermead/sbplx.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/neldermead/sbplx.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/newuoa/newuoa.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/newuoa/newuoa.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/praxis/praxis.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/praxis/praxis.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/util/redblack.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/util/redblack.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/util/rescale.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/util/rescale.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/util/stop.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/util/stop.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/util/timer.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/util/timer.c | |
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| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/util/sobolseq.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/util/sobolseq.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/nlopt.dir/util/mt19937ar.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/nlopt/util/mt19937ar.c | |
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| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/ErrorHandling.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/LineIterator.cpp | |
| Scanning dependencies of target dev_support | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/MemoryBuffer.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/Mutex.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/Mutex.cpp | |
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| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/Path.cpp | |
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| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/Regex.cpp | |
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| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/BamAlignment.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/BamAlignment.cpp | |
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| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/Signals.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/SamHeader.cpp | |
| make -f modules/dev_support/CMakeFiles/dev_support.dir/build.make modules/dev_support/CMakeFiles/dev_support.dir/build | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/SmallVector.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/BamMultiReader.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/SourceMgr.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/StringMap.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/BamReader.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/StringRef.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/BamWriter.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/Twine.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/SamProgram.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/SamProgram.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/YAMLParser.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/SamProgramChain.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/YAMLTraits.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/raw_ostream.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/SamReadGroup.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/regcomp.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/SamReadGroupDictionary.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/SamSequence.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/SamSequence.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/regerror.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/regerror.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/regexec.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/regexec.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/SamSequenceDictionary.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/regfree.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/regfree.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/llvm/regstrlcpy.c | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o | |
| [ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o | |
| [ 25%] Building CXX object modules/dev_support/CMakeFiles/dev_support.dir/copy_file.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/dev_support && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/dev_support -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/dev_support -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/dev_support.dir/copy_file.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/dev_support/copy_file.cpp | |
| [ 27%] Building CXX object modules/dev_support/CMakeFiles/dev_support.dir/path_helper.cpp.o | |
| [ 27%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/dev_support && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/dev_support -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/dev_support -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/dev_support.dir/path_helper.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/dev_support/path_helper.cpp | |
| [ 27%] Building CXX object modules/dev_support/CMakeFiles/dev_support.dir/logger/logger_impl.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/dev_support && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/dev_support -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/dev_support -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/dev_support.dir/logger/logger_impl.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/dev_support/logger/logger_impl.cpp | |
| [ 28%] Linking C static library libhattrie.a | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -P CMakeFiles/hattrie.dir/cmake_clean_target.cmake | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/htrie && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_link_script CMakeFiles/hattrie.dir/link.txt --verbose=1 | |
| /bio/linuxbrew/bin/ar qc libhattrie.a CMakeFiles/hattrie.dir/ahtable.c.o CMakeFiles/hattrie.dir/hat-trie.c.o CMakeFiles/hattrie.dir/misc.c.o CMakeFiles/hattrie.dir/murmurhash3.c.o | |
| /bio/linuxbrew/bin/ranlib libhattrie.a | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 28%] Built target hattrie | |
| make -f modules/assembly_graph/CMakeFiles/graph_support.dir/build.make modules/assembly_graph/CMakeFiles/graph_support.dir/depend | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/assembly_graph /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/assembly_graph /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/assembly_graph/CMakeFiles/graph_support.dir/DependInfo.cmake --color= | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/bam/BamHeader_p.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp | |
| [ 28%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bamlite.c.o | |
| [ 28%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwa.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwa.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwa.c | |
| [ 29%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwamem.c.o | |
| [ 28%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bamlite.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bamlite.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwamem.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwamem.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/bam/BamReader_p.cpp | |
| [ 30%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwashm.c.o | |
| [ 29%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwase.c.o | |
| [ 29%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o | |
| [ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/index/BamIndexFactory_p.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwase.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwase.c | |
| [ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o | |
| [ 32%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o | |
| [ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwashm.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwashm.c | |
| [ 32%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwt_lite.c.o | |
| [ 32%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/bam/BamWriter_p.cpp | |
| [ 31%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwtgap.c.o | |
| [ 35%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwtsw2_pair.c.o | |
| [ 36%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o | |
| [ 35%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwtsw2_core.c.o | |
| [ 35%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwtsw2_aux.c.o | |
| [ 35%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o | |
| [ 33%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwtaln.c.o | |
| [ 33%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o | |
| [ 34%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwtindex.c.o | |
| [ 33%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwt_lite.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwt_lite.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/index/BamStandardIndex_p.cpp | |
| [ 36%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp | |
| [ 36%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/fastmap.c.o | |
| [ 36%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwtaln.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwtaln.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/BamFile_p.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwtgap.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwtgap.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwtindex.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwtindex.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/ByteArray_p.cpp | |
| Scanning dependencies of target jemalloc | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwtsw2_aux.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwtsw2_aux.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/ILocalIODevice_p.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwtsw2_core.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwtsw2_core.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/ParallelBgzfStream_p.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/RollingBuffer_p.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwtsw2_pair.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwtsw2_pair.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/fastmap.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/fastmap.c | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make -f ext/jemalloc/CMakeFiles/jemalloc.dir/build.make ext/jemalloc/CMakeFiles/jemalloc.dir/build | |
| Scanning dependencies of target algorithms | |
| Scanning dependencies of target graph_support | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make -f modules/algorithms/CMakeFiles/algorithms.dir/build.make modules/algorithms/CMakeFiles/algorithms.dir/build | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make -f modules/assembly_graph/CMakeFiles/graph_support.dir/build.make modules/assembly_graph/CMakeFiles/graph_support.dir/build | |
| Scanning dependencies of target stages | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make -f modules/stages/CMakeFiles/stages.dir/build.make modules/stages/CMakeFiles/stages.dir/build | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 36%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/arena.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/arena.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/arena.c | |
| [ 36%] Building CXX object modules/assembly_graph/CMakeFiles/graph_support.dir/components/connected_component.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/assembly_graph && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/assembly_graph -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/assembly_graph -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/graph_support.dir/components/connected_component.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/assembly_graph/components/connected_component.cpp | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 37%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/gcc-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c | |
| [ 38%] Building CXX object modules/algorithms/CMakeFiles/algorithms.dir/genome_consistance_checker.cpp.o | |
| [ 38%] Building CXX object modules/stages/CMakeFiles/stages.dir/construction.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/stages && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/stages -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/stages -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/stages.dir/construction.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/stages/construction.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/algorithms && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/algorithms -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/algorithms -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/algorithms.dir/genome_consistance_checker.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/algorithms/genome_consistance_checker.cpp | |
| [ 38%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/base.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/base.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/base.c | |
| [ 39%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/kstring.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/kstring.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/kstring.c | |
| [ 40%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/chunk.c | |
| [ 40%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk_mmap.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk_mmap.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/chunk_mmap.c | |
| [ 41%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/ctl.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/ctl.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/ctl.c | |
| [ 41%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/main.c.o | |
| [ 42%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/utils.c.o | |
| [ 42%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/hash.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/hash.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/hash.c | |
| [ 42%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/jemalloc.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/jemalloc.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/jemalloc.c | |
| [ 43%] Linking C static library libnlopt.a | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -P CMakeFiles/nlopt.dir/cmake_clean_target.cmake | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/nlopt && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_link_script CMakeFiles/nlopt.dir/link.txt --verbose=1 | |
| /bio/linuxbrew/bin/ar qc libnlopt.a CMakeFiles/nlopt.dir/api/general.c.o CMakeFiles/nlopt.dir/api/optimize.c.o CMakeFiles/nlopt.dir/api/options.c.o CMakeFiles/nlopt.dir/api/deprecated.c.o CMakeFiles/nlopt.dir/auglag/auglag.c.o CMakeFiles/nlopt.dir/bobyqa/bobyqa.c.o CMakeFiles/nlopt.dir/cdirect/cdirect.c.o CMakeFiles/nlopt.dir/cdirect/hybrid.c.o CMakeFiles/nlopt.dir/cobyla/cobyla.c.o CMakeFiles/nlopt.dir/crs/crs.c.o CMakeFiles/nlopt.dir/esch/esch.c.o CMakeFiles/nlopt.dir/isres/isres.c.o CMakeFiles/nlopt.dir/mma/mma.c.o CMakeFiles/nlopt.dir/mma/ccsa_quadratic.c.o CMakeFiles/nlopt.dir/mlsl/mlsl.c.o CMakeFiles/nlopt.dir/neldermead/nldrmd.c.o CMakeFiles/nlopt.dir/neldermead/sbplx.c.o CMakeFiles/nlopt.dir/newuoa/newuoa.c.o CMakeFiles/nlopt.dir/praxis/praxis.c.o CMakeFiles/nlopt.dir/util/redblack.c.o CMakeFiles/nlopt.dir/util/rescale.c.o CMakeFiles/nlopt.dir/util/stop.c.o CMakeFiles/nlopt.dir/util/timer.c.o CMakeFiles/nlopt.dir/util/qsort_r.c.o CMakeFiles/nlopt.dir/util/sobolseq.c.o CMakeFiles/nlopt.dir/util/mt19937ar.c.o | |
| /bio/linuxbrew/bin/ranlib libnlopt.a | |
| [ 43%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/gcc-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 43%] Built target nlopt | |
| make -f modules/math/CMakeFiles/math_module.dir/build.make modules/math/CMakeFiles/math_module.dir/depend | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/main.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/main.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/utils.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/utils.c | |
| [ 43%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/math /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/math /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/math/CMakeFiles/math_module.dir/DependInfo.cmake --color= | |
| [ 43%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bntseq.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bntseq.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bntseq.c | |
| [ 44%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/mutex.c.o | |
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| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/stages && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/stages -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/stages -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/stages.dir/simplification.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/stages/simplification.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/mutex.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/mutex.c | |
| [ 45%] Building CXX object modules/assembly_graph/CMakeFiles/graph_support.dir/paths/bidirectional_path.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/assembly_graph && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/assembly_graph -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/assembly_graph -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/graph_support.dir/paths/bidirectional_path.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/assembly_graph/paths/bidirectional_path.cpp | |
| [ 45%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/quarantine.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/quarantine.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/quarantine.c | |
| [ 45%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/stats.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/stats.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/stats.c | |
| [ 46%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/tsd.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/tsd.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/tsd.c | |
| [ 46%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwape.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwape.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwape.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/gcc-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/pbgzf/block.c | |
| Scanning dependencies of target math_module | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make -f modules/math/CMakeFiles/math_module.dir/build.make modules/math/CMakeFiles/math_module.dir/build | |
| [ 48%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwaseqio.c.o | |
| [ 47%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/atomic.c.o | |
| [ 48%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwaseqio.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwaseqio.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/atomic.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/atomic.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/gcc-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/pbgzf/consumer.c | |
| make[2]: Entering directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 48%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/gcc-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c | |
| [ 49%] Building CXX object modules/math/CMakeFiles/math_module.dir/kmer_coverage_model.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/math && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/math -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/math -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/math_module.dir/kmer_coverage_model.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/math/kmer_coverage_model.cpp | |
| [ 49%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/bitmap.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/bitmap.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/bitmap.c | |
| [ 49%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwt.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwt.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwt.c | |
| [ 50%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk_dss.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk_dss.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/chunk_dss.c | |
| [ 51%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/gcc-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/pbgzf/queue.c | |
| [ 51%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/ckh.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/ckh.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/ckh.c | |
| [ 51%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/gcc-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/pbgzf/reader.c | |
| [ 52%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/extent.c.o | |
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| [ 52%] Building CXX object modules/assembly_graph/CMakeFiles/graph_support.dir/graph_support/scaff_supplementary.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/assembly_graph && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/assembly_graph -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/assembly_graph -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/graph_support.dir/graph_support/scaff_supplementary.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules/assembly_graph/graph_support/scaff_supplementary.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwt_gen.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwt_gen.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/extent.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/extent.c | |
| [ 52%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/gcc-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/pbgzf/util.c | |
| [ 53%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/gcc-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/io/pbgzf/writer.c | |
| [ 53%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o | |
| [ 53%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/huge.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/huge.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/huge.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp | |
| [ 53%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/mb.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/mb.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/mb.c | |
| [ 54%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o | |
| [ 53%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o | |
| [ 55%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwtsw2_chain.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwtsw2_chain.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwtsw2_chain.c | |
| [ 56%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/prof.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/prof.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/prof.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp | |
| [ 56%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/rtree.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/rtree.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/rtree.c | |
| [ 56%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwtsw2_main.c.o | |
| [ 56%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwtsw2_main.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwtsw2_main.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api && /bio/linuxbrew/bin/g++-5 -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/src -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/bamtools/api/internal/utils/BamException_p.cpp | |
| [ 56%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/tcache.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/tcache.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/tcache.c | |
| [ 56%] Linking CXX static library libssw.a | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ssw && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -P CMakeFiles/ssw.dir/cmake_clean_target.cmake | |
| [ 57%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/util.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc && /bio/linuxbrew/bin/gcc-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/util.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/jemalloc/util.c | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ssw && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_link_script CMakeFiles/ssw.dir/link.txt --verbose=1 | |
| [ 57%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/is.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/is.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/is.c | |
| [ 58%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/ksw.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/ksw.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/ksw.c | |
| /bio/linuxbrew/bin/ar qc libssw.a CMakeFiles/ssw.dir/ssw.c.o CMakeFiles/ssw.dir/ssw_cpp.cpp.o | |
| [ 58%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/pemerge.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/pemerge.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/pemerge.c | |
| [ 59%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/QSufSort.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/QSufSort.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/QSufSort.c | |
| /bio/linuxbrew/bin/ranlib libssw.a | |
| [ 59%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/kopen.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/kopen.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/kopen.c | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 59%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwamem_extra.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwamem_extra.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwamem_extra.c | |
| [ 59%] Built target ssw | |
| [ 60%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/bwamem_pair.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/bwamem_pair.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/bwamem_pair.c | |
| [ 60%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/kthread.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/kthread.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/kthread.c | |
| [ 60%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/bwa-spades.dir/malloc_wrap.c.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/bin/gcc-5 -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -Os -w -pipe -march=native -fopenmp -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/bwa-spades.dir/malloc_wrap.c.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/tools/bwa-0.7.12/malloc_wrap.c | |
| In file included from /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cityhash/city.cc:509:0: | |
| /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/include/city/citycrc.h:34:1: error: 'uint128' does not name a type | |
| uint128 CityHashCrc128(const char *s, size_t len); | |
| ^ | |
| /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/include/city/citycrc.h:38:1: error: 'uint128' does not name a type | |
| uint128 CityHashCrc128WithSeed(const char *s, size_t len, uint128 seed); | |
| ^ | |
| /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/include/city/citycrc.h:41:48: error: 'uint64' has not been declared | |
| void CityHashCrc256(const char *s, size_t len, uint64 *result); | |
| ^ | |
| /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cityhash/city.cc: In function 'void CityHashCrc256Short(const char*, size_t, uint64_t*)': | |
| /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cityhash/city.cc:605:45: error: 'uint32' does not name a type | |
| CityHashCrc256Long(buf, 240, ~static_cast<uint32>(len), result); | |
| ^ | |
| /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cityhash/city.cc: In function 'city_uint128 CityHashCrc128WithSeed(const char*, size_t, city_uint128)': | |
| /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cityhash/city.cc:625:64: error: 'uint128' was not declared in this scope | |
| HashLen16(Rotate(v, 32), u * k0 + result[3])); | |
| ^ | |
| /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cityhash/city.cc: In function 'city_uint128 CityHashCrc128(const char*, size_t)': | |
| /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/cityhash/city.cc:635:40: error: 'uint128' was not declared in this scope | |
| return uint128(result[2], result[3]); | |
| ^ | |
| make[2]: *** [ext/cityhash/CMakeFiles/cityhash.dir/build.make:66: ext/cityhash/CMakeFiles/cityhash.dir/city.cc.o] Error 1 | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make[1]: *** [CMakeFiles/Makefile2:793: ext/cityhash/CMakeFiles/cityhash.dir/all] Error 2 | |
| make[1]: *** Waiting for unfinished jobs.... | |
| [ 61%] Linking C executable ../../bin/bwa-spades | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext_tools/bwa-0.7.12 && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_link_script CMakeFiles/bwa-spades.dir/link.txt --verbose=1 | |
| /bio/linuxbrew/bin/gcc-5 -Os -w -pipe -march=native -fopenmp -DNDEBUG -L/bio/linuxbrew/lib -Wl,--dynamic-linker=/bio/linuxbrew/lib/ld.so -Wl,-rpath,/bio/linuxbrew/lib CMakeFiles/bwa-spades.dir/bamlite.c.o CMakeFiles/bwa-spades.dir/bwa.c.o CMakeFiles/bwa-spades.dir/bwamem.c.o CMakeFiles/bwa-spades.dir/bwase.c.o CMakeFiles/bwa-spades.dir/bwashm.c.o CMakeFiles/bwa-spades.dir/bwtaln.c.o CMakeFiles/bwa-spades.dir/bwtgap.c.o CMakeFiles/bwa-spades.dir/bwtindex.c.o CMakeFiles/bwa-spades.dir/bwt_lite.c.o CMakeFiles/bwa-spades.dir/bwtsw2_aux.c.o CMakeFiles/bwa-spades.dir/bwtsw2_core.c.o CMakeFiles/bwa-spades.dir/bwtsw2_pair.c.o CMakeFiles/bwa-spades.dir/fastmap.c.o CMakeFiles/bwa-spades.dir/kstring.c.o CMakeFiles/bwa-spades.dir/main.c.o CMakeFiles/bwa-spades.dir/utils.c.o CMakeFiles/bwa-spades.dir/bntseq.c.o CMakeFiles/bwa-spades.dir/bwape.c.o CMakeFiles/bwa-spades.dir/bwaseqio.c.o CMakeFiles/bwa-spades.dir/bwt.c.o CMakeFiles/bwa-spades.dir/bwt_gen.c.o CMakeFiles/bwa-spades.dir/bwtsw2_chain.c.o CMakeFiles/bwa-spades.dir/bwtsw2_main.c.o CMakeFiles/bwa-spades.dir/is.c.o CMakeFiles/bwa-spades.dir/ksw.c.o CMakeFiles/bwa-spades.dir/pemerge.c.o CMakeFiles/bwa-spades.dir/QSufSort.c.o CMakeFiles/bwa-spades.dir/kopen.c.o CMakeFiles/bwa-spades.dir/bwamem_extra.c.o CMakeFiles/bwa-spades.dir/bwamem_pair.c.o CMakeFiles/bwa-spades.dir/kthread.c.o CMakeFiles/bwa-spades.dir/malloc_wrap.c.o -o ../../bin/bwa-spades -rdynamic -lz -lm -lrt | |
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| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include/ConsensusCore -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/ConsensusCore.dir/Features.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore/Features.cpp | |
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| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include/ConsensusCore -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore/Sequence.cpp | |
| [ 65%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include/ConsensusCore -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/ConsensusCore.dir/Utils.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore/Utils.cpp | |
| [ 65%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o | |
| [ 65%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o | |
| [ 66%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o | |
| [ 66%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include/ConsensusCore -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/ConsensusCore.dir/Version.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore/Version.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include/ConsensusCore -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore/Matrix/DenseMatrix.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include/ConsensusCore -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore/Matrix/SparseMatrix.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include/ConsensusCore -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore/Poa/PoaConfig.cpp | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include/ConsensusCore -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore/Poa/PoaConsensus.cpp | |
| [ 67%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore && /bio/linuxbrew/bin/g++-5 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/modules -isystem /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include -isystem /bio/linuxbrew/include -I/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/../ext/include/ConsensusCore -Os -w -pipe -march=native -fopenmp -std=c++11 -DNDEBUG -Wno-deprecated -g0 -O2 -o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -c /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/ext/src/ConsensusCore/Poa/PoaGraph.cpp | |
| [ 67%] Linking CXX static library libmath_module.a | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/math && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -P CMakeFiles/math_module.dir/cmake_clean_target.cmake | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/math && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_link_script CMakeFiles/math_module.dir/link.txt --verbose=1 | |
| /bio/linuxbrew/bin/ar qc libmath_module.a CMakeFiles/math_module.dir/kmer_coverage_model.cpp.o | |
| /bio/linuxbrew/bin/ranlib libmath_module.a | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 67%] Built target math_module | |
| [ 67%] Linking CXX static library libgraph_support.a | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/assembly_graph && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -P CMakeFiles/graph_support.dir/cmake_clean_target.cmake | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/assembly_graph && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_link_script CMakeFiles/graph_support.dir/link.txt --verbose=1 | |
| /bio/linuxbrew/bin/ar qc libgraph_support.a CMakeFiles/graph_support.dir/components/connected_component.cpp.o CMakeFiles/graph_support.dir/paths/bidirectional_path.cpp.o CMakeFiles/graph_support.dir/graph_support/scaff_supplementary.cpp.o | |
| /bio/linuxbrew/bin/ranlib libgraph_support.a | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 67%] Built target graph_support | |
| [ 68%] Linking CXX static library libalgorithms.a | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/algorithms && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -P CMakeFiles/algorithms.dir/cmake_clean_target.cmake | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/algorithms && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_link_script CMakeFiles/algorithms.dir/link.txt --verbose=1 | |
| /bio/linuxbrew/bin/ar qc libalgorithms.a CMakeFiles/algorithms.dir/genome_consistance_checker.cpp.o | |
| /bio/linuxbrew/bin/ranlib libalgorithms.a | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 68%] Built target algorithms | |
| [ 68%] Linking CXX static library libConsensusCore.a | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/ext/ConsensusCore && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 | |
| /bio/linuxbrew/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Feature.cpp.o CMakeFiles/ConsensusCore.dir/Features.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o | |
| /bio/linuxbrew/bin/ranlib libConsensusCore.a | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 68%] Built target ConsensusCore | |
| [ 69%] Linking CXX static library libstages.a | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/stages && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -P CMakeFiles/stages.dir/cmake_clean_target.cmake | |
| cd /tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build/modules/stages && /bio/linuxbrew/Cellar/cmake/3.5.2/bin/cmake -E cmake_link_script CMakeFiles/stages.dir/link.txt --verbose=1 | |
| /bio/linuxbrew/bin/ar qc libstages.a CMakeFiles/stages.dir/construction.cpp.o CMakeFiles/stages.dir/simplification.cpp.o | |
| /bio/linuxbrew/bin/ranlib libstages.a | |
| make[2]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| [ 69%] Built target stages | |
| make[1]: Leaving directory '/tmp/spades-20160601-9085-1rlp57i/SPAdes-3.8.0/src/build' | |
| make: *** [Makefile:153: all] Error 2 | |
| HOMEBREW_VERSION: 0.9.9 | |
| ORIGIN: https://github.com/Linuxbrew/brew.git | |
| HEAD: 68c10e47400571d20c1c6dc407a7d9b7c32ba79a | |
| Last commit: 4 days ago | |
| Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core | |
| Core tap HEAD: 91737fc35c3023ef52d9696505e41639c59072a1 | |
| Core tap last commit: 37 minutes ago | |
| HOMEBREW_PREFIX: /bio/linuxbrew | |
| HOMEBREW_REPOSITORY: /bio/linuxbrew | |
| HOMEBREW_CELLAR: /bio/linuxbrew/Cellar | |
| HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com | |
| CPU: 72-core 64-bit haswell | |
| Kernel: Linux 3.10.0-327.18.2.el7.x86_64 x86_64 GNU/Linux | |
| OS: Red Hat Enterprise Linux Server release 7.2 (Maipo) | |
| Codename: Maipo | |
| OS glibc: 2.17 | |
| OS gcc: 4.8.5 | |
| Linuxbrew glibc: N/A | |
| Linuxbrew gcc: 5.3.0 | |
| Clang: N/A | |
| X11: N/A | |
| System Ruby: 2.3.0 => /bio/linuxbrew/Cellar/ruby/2.3.0/bin/ruby | |
| Perl: /usr/bin/perl | |
| Python: /bio/linuxbrew/bin/python => /bio/linuxbrew/Cellar/python/2.7.11/bin/python2.7 | |
| Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.3.0/bin/ruby | |
| Java: openjdk version "1.8.0_91" | |
| CC: /bio/linuxbrew/bin/gcc-5 => /bio/linuxbrew/Cellar/gcc/5.3.0/bin/gcc-5 | |
| CXX: /bio/linuxbrew/bin/g++-5 => /bio/linuxbrew/Cellar/gcc/5.3.0/bin/g++-5 | |
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| CXXFLAGS: -Os -w -pipe -march=native | |
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| LDFLAGS: -L/bio/linuxbrew/lib -Wl,--dynamic-linker=/bio/linuxbrew/lib/ld.so -Wl,-rpath,/bio/linuxbrew/lib | |
| MAKEFLAGS: -j72 | |
| CMAKE_PREFIX_PATH: /bio/linuxbrew | |
| PKG_CONFIG_LIBDIR: /bio/linuxbrew/lib/pkgconfig:/bio/linuxbrew/share/pkgconfig | |
| HOMEBREW_BUILD_FROM_SOURCE: 1 | |
| PATH: /bio/linuxbrew/bin:/home/tseemann/perl5/bin:/bio/perl5/bin:/bio/linuxbrew/bin:/bio/linuxbrew/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bio/sw/hierBAPS:/bio/sw/brat:/bio/sw/mauve:/bio/sw/splitstree4:/bio/sw/vbc/fqa-tools:/bio/sw/vbc/misc:/bio/sw/tablet:/home/tseemann/git/wombac/bin:/home/tseemann/git/snippy/bin:/home/tseemann/git/barrnap/bin:/home/tseemann/git/nullarbor/bin:/home/tseemann/git/prokka/bin:/home/tseemann/git/mlst/bin:/home/tseemann/git/abricate/bin:/home/tseemann/git/mdu-tools/bin:/usr/local/sbin:/usr/sbin:/home/tseemann/.local/bin:/home/tseemann/bin:/bio/linuxbrew/Library/ENV/scm | |
| CPATH: /bio/linuxbrew/include | |
| LD_LIBRARY_PATH: /bio/linuxbrew/Cellar/spades/3.8.0/lib:/bio/linuxbrew/Cellar/spades/3.8.0 | |
| LD_RUN_PATH: /bio/linuxbrew/lib | |
| LIBRARY_PATH: /bio/linuxbrew/lib |
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