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September 25, 2016 20:50
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abyss (homebrew/science/abyss) on 2.6.32-573.8.1.el6.x86_64 - Homebrew build logs
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| Homebrew build logs for homebrew/science/abyss on 2.6.32-573.8.1.el6.x86_64 | |
| Build date: 2016-09-25 13:48:38 |
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| HOMEBREW_VERSION: 0.9.9 | |
| ORIGIN: https://github.com/Linuxbrew/brew.git | |
| HEAD: 28c79defe0ed12f524998a68f22c19ab058b288f | |
| Last commit: 64 minutes ago | |
| Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core | |
| Core tap HEAD: 600e2df32333a66f21d60437446c68e4716a60c5 | |
| Core tap last commit: 23 hours ago | |
| HOMEBREW_PREFIX: /gsc/btl/linuxbrew | |
| HOMEBREW_REPOSITORY: /gsc/btl/linuxbrew | |
| HOMEBREW_CELLAR: /gsc/btl/linuxbrew/Cellar | |
| HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com | |
| CPU: 32-core 64-bit haswell | |
| Homebrew Ruby: 2.3.0 => /gsc/btl/linuxbrew/Cellar/ruby/2.3.0/bin/ruby | |
| Clang: 3.8 build 0 | |
| Git: 2.8.2 => /gsc/btl/linuxbrew/bin/git | |
| Perl: /gsc/btl/linuxbrew/bin/perl => /gsc/btl/linuxbrew/Cellar/perl/5.24.0_1/bin/perl | |
| Python: /gsc/btl/linuxbrew/bin/python => /gsc/btl/linuxbrew/Cellar/python/2.7.12_1/bin/python2.7 | |
| Ruby: /gsc/btl/linuxbrew/bin/ruby => /gsc/btl/linuxbrew/Cellar/ruby/2.3.0/bin/ruby | |
| Java: 1.8.0_102 | |
| Kernel: Linux 2.6.32-573.8.1.el6.x86_64 x86_64 GNU/Linux | |
| OS: CentOS release 6.7 (Final) | |
| OS glibc: 2.12 | |
| OS gcc: 4.4.7 | |
| Linuxbrew glibc: 2.19 | |
| Linuxbrew gcc: 5.3.0 | |
| Linuxbrew xorg: 20160314 |
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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: | |
| git | |
| gcc48 | |
| abyss | |
| r | |
| jdk7 | |
| samtools-0.1 | |
| pbsuite | |
| quorum | |
| ncbi-c++-toolkit | |
| gcc49 | |
| numpy | |
| gcc5 | |
| remake | |
| masurca | |
| amos | |
| populations | |
| scalapack | |
| lapack | |
| discovardenovo | |
| libelf | |
| Warning: Some installed formula are missing dependencies. | |
| You should `brew install` the missing dependencies: | |
| brew install igraph | |
| Run `brew missing` for more details. |
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| Formula: abyss | |
| Tap: homebrew/science | |
| Path: /gsc/btl/linuxbrew/Library/Taps/homebrew/homebrew-science/abyss.rb |
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| 2016-09-25 13:46:06 -0700 | |
| ./configure | |
| --enable-maxk=160 | |
| --prefix=/gsc/btl/linuxbrew/Cellar/abyss/2.0.1 | |
| --disable-dependency-tracking | |
| checking for a BSD-compatible install... /gsc/btl/linuxbrew/bin/ginstall -c | |
| checking whether build environment is sane... yes | |
| checking for a thread-safe mkdir -p... /gsc/btl/linuxbrew/bin/mkdir -p | |
| checking for gawk... gawk | |
| checking whether make sets $(MAKE)... yes | |
| checking whether make supports nested variables... yes | |
| checking for gawk... (cached) gawk | |
| checking for gcc... /gsc/btl/linuxbrew/bin/gcc-5 | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.out | |
| checking for suffix of executables... | |
| checking whether we are cross compiling... no | |
| checking for suffix of object files... o | |
| checking whether we are using the GNU C compiler... yes | |
| checking whether /gsc/btl/linuxbrew/bin/gcc-5 accepts -g... yes | |
| checking for /gsc/btl/linuxbrew/bin/gcc-5 option to accept ISO C89... none needed | |
| checking for style of include used by make... GNU | |
| checking dependency style of /gsc/btl/linuxbrew/bin/gcc-5... none | |
| checking how to run the C preprocessor... /gsc/btl/linuxbrew/bin/gcc-5 -E | |
| checking whether we are using the GNU C++ compiler... yes | |
| checking whether /gsc/btl/linuxbrew/bin/g++-5 accepts -g... yes | |
| checking dependency style of /gsc/btl/linuxbrew/bin/g++-5... none | |
| checking for ranlib... ranlib | |
| checking for ghc... ghc | |
| checking for ghc-pkg... ghc-pkg | |
| checking for pandoc... yes | |
| checking for grep that handles long lines and -e... /gsc/btl/linuxbrew/bin/grep | |
| checking for egrep... /gsc/btl/linuxbrew/bin/grep -E | |
| checking for ANSI C header files... yes | |
| checking for sys/types.h... yes | |
| checking for sys/stat.h... yes | |
| checking for stdlib.h... yes | |
| checking for string.h... yes | |
| checking for memory.h... yes | |
| checking for strings.h... yes | |
| checking for inttypes.h... yes | |
| checking for stdint.h... yes | |
| checking for unistd.h... yes | |
| checking dlfcn.h usability... yes | |
| checking dlfcn.h presence... yes | |
| checking for dlfcn.h... yes | |
| checking fcntl.h usability... yes | |
| checking fcntl.h presence... yes | |
| checking for fcntl.h... yes | |
| checking float.h usability... yes | |
| checking float.h presence... yes | |
| checking for float.h... yes | |
| checking limits.h usability... yes | |
| checking limits.h presence... yes | |
| checking for limits.h... yes | |
| checking stddef.h usability... yes | |
| checking stddef.h presence... yes | |
| checking for stddef.h... yes | |
| checking for stdint.h... (cached) yes | |
| checking for stdlib.h... (cached) yes | |
| checking sys/param.h usability... yes | |
| checking sys/param.h presence... yes | |
| checking for sys/param.h... yes | |
| checking for stdbool.h that conforms to C99... yes | |
| checking for _Bool... yes | |
| checking for ANSI C header files... (cached) yes | |
| checking whether byte ordering is bigendian... no | |
| checking for an ANSI C-conforming const... yes | |
| checking for inline... inline | |
| checking for ptrdiff_t... yes | |
| checking for mode_t... yes | |
| checking for pid_t... yes | |
| checking for size_t... yes | |
| checking for ssize_t... yes | |
| checking for int64_t... yes | |
| checking for uint8_t... yes | |
| checking for uint16_t... yes | |
| checking for uint32_t... yes | |
| checking for uint64_t... yes | |
| checking for std::hash<int>... no | |
| checking for std::tr1::hash<int>... yes | |
| checking for dup2... yes | |
| checking for gethostname... yes | |
| checking for getopt_long... yes | |
| checking for getpagesize... yes | |
| checking for memset... yes | |
| checking for strdup... yes | |
| checking for strerror... yes | |
| checking for strtoul... yes | |
| checking vfork.h usability... no | |
| checking vfork.h presence... no | |
| checking for vfork.h... no | |
| checking for fork... yes | |
| checking for vfork... yes | |
| checking for working fork... yes | |
| checking for working vfork... (cached) yes | |
| checking for stdlib.h... (cached) yes | |
| checking for GNU libc compatible malloc... yes | |
| checking for working memcmp... yes | |
| checking for stdlib.h... (cached) yes | |
| checking for GNU libc compatible realloc... yes | |
| checking for vprintf... yes | |
| checking for _doprnt... no | |
| checking whether HOST_NAME_MAX is declared... yes | |
| checking build system type... x86_64-unknown-linux-gnu | |
| checking host system type... x86_64-unknown-linux-gnu | |
| checking if compiler needs -Werror to reject unknown flags... no | |
| checking for the pthreads library -lpthreads... no | |
| checking whether pthreads work without any flags... no | |
| checking whether pthreads work with -Kthread... no | |
| checking whether pthreads work with -kthread... no | |
| checking for the pthreads library -llthread... no | |
| checking whether pthreads work with -pthread... yes | |
| checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE | |
| checking if more special flags are required for pthreads... no | |
| checking for PTHREAD_PRIO_INHERIT... yes | |
| checking mpi.h usability... yes | |
| checking mpi.h presence... yes | |
| checking for mpi.h... yes | |
| checking for MPI_Init in -lmpi... yes | |
| checking for sqrt in -lm... yes | |
| checking for pow... yes | |
| checking for sqrt... yes | |
| checking for ceilf... yes | |
| checking for dlsym in -ldl... yes | |
| checking how to run the C++ preprocessor... /gsc/btl/linuxbrew/bin/g++-5 -E | |
| checking functional usability... yes | |
| checking functional presence... yes | |
| checking for functional... yes | |
| checking tr1/functional usability... yes | |
| checking tr1/functional presence... yes | |
| checking for tr1/functional... yes | |
| checking boost/functional/hash.hpp usability... yes | |
| checking boost/functional/hash.hpp presence... yes | |
| checking for boost/functional/hash.hpp... yes | |
| checking boost/property_map/property_map.hpp usability... yes | |
| checking boost/property_map/property_map.hpp presence... yes | |
| checking for boost/property_map/property_map.hpp... yes | |
| checking google/sparse_hash_map usability... yes | |
| checking google/sparse_hash_map presence... yes | |
| checking for google/sparse_hash_map... yes | |
| checking unordered_map usability... no | |
| checking unordered_map presence... no | |
| checking for unordered_map... no | |
| checking tr1/unordered_map usability... yes | |
| checking tr1/unordered_map presence... yes | |
| checking for tr1/unordered_map... yes | |
| checking unordered_set usability... no | |
| checking unordered_set presence... no | |
| checking for unordered_set... no | |
| checking tr1/unordered_set usability... yes | |
| checking tr1/unordered_set presence... yes | |
| checking for tr1/unordered_set... yes | |
| checking boost/unordered_set.hpp usability... yes | |
| checking boost/unordered_set.hpp presence... yes | |
| checking for boost/unordered_set.hpp... yes | |
| checking sqlite3.h usability... yes | |
| checking sqlite3.h presence... yes | |
| checking for sqlite3.h... yes | |
| checking for main in -lsqlite3... yes | |
| checking for /gsc/btl/linuxbrew/bin/g++-5 option to support OpenMP... -fopenmp | |
| checking that generated files are newer than configure... done | |
| configure: creating ./config.status | |
| config.status: creating Makefile | |
| config.status: creating ABYSS/Makefile | |
| config.status: creating Align/Makefile | |
| config.status: creating Assembly/Makefile | |
| config.status: creating Common/Makefile | |
| config.status: creating DataLayer/Makefile | |
| config.status: creating FMIndex/Makefile | |
| config.status: creating Graph/Makefile | |
| config.status: creating Parallel/Makefile | |
| config.status: creating bin/Makefile | |
| config.status: creating doc/Makefile | |
| config.status: creating dialign/Makefile | |
| config.status: creating kmerprint/Makefile | |
| config.status: creating AdjList/Makefile | |
| config.status: creating Konnector/Makefile | |
| config.status: creating DAssembler/Makefile | |
| config.status: creating DistanceEst/Makefile | |
| config.status: creating Layout/Makefile | |
| config.status: creating Map/Makefile | |
| config.status: creating Misc/Makefile | |
| config.status: creating Overlap/Makefile | |
| config.status: creating PopBubbles/Makefile | |
| config.status: creating Scaffold/Makefile | |
| config.status: creating SimpleGraph/Makefile | |
| config.status: creating MergePaths/Makefile | |
| config.status: creating KAligner/Makefile | |
| config.status: creating PairedDBG/Makefile | |
| config.status: creating ParseAligns/Makefile | |
| config.status: creating PathOverlap/Makefile | |
| config.status: creating Consensus/Makefile | |
| config.status: creating FilterGraph/Makefile | |
| config.status: creating GapFiller/Makefile | |
| config.status: creating Sealer/Makefile | |
| config.status: creating lib/gtest-1.7.0/Makefile | |
| config.status: creating Unittest/Makefile | |
| config.status: creating LogKmerCount/Makefile | |
| config.status: creating Bloom/Makefile | |
| config.status: creating BloomDBG/Makefile | |
| config.status: creating DataBase/Makefile | |
| config.status: creating lib/bloomfilter/Makefile | |
| config.status: creating lib/rolling-hash/Makefile | |
| config.status: creating config.h | |
| config.status: executing depfiles commands |
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| 2016-09-25 13:46:22 -0700 | |
| make | |
| make all-recursive | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1' | |
| Making all in bin | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/bin' | |
| make[2]: Nothing to be done for 'all'. | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/bin' | |
| Making all in doc | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/doc' | |
| make[2]: Nothing to be done for 'all'. | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/doc' | |
| Making all in Common | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Common' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc | |
| rm -f libcommon.a | |
| ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o | |
| ranlib libcommon.a | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Common' | |
| Making all in Graph | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Graph' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L. -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Graph' | |
| Making all in DataLayer | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DataLayer' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc | |
| rm -f libdatalayer.a | |
| ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o | |
| ranlib libdatalayer.a | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DataLayer' | |
| Making all in DataBase | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DataBase' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc | |
| rm -f libdb.a | |
| ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a | |
| ranlib libdb.a | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DataBase' | |
| Making all in FMIndex | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/FMIndex' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc | |
| rm -f libfmindex.a | |
| ar cru libfmindex.a libfmindex_a-bit_array.o | |
| ranlib libfmindex.a | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/FMIndex' | |
| Making all in Assembly | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Assembly' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc | |
| rm -f libassembly.a | |
| ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a | |
| ranlib libassembly.a | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Assembly' | |
| Making all in dialign | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/dialign' | |
| /gsc/btl/linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Os -w -pipe -march=native -c -o alig.o alig.c | |
| /gsc/btl/linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Os -w -pipe -march=native -c -o assemble.o assemble.c | |
| /gsc/btl/linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Os -w -pipe -march=native -c -o diag.o diag.c | |
| /gsc/btl/linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Os -w -pipe -march=native -c -o io.o io.c | |
| /gsc/btl/linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Os -w -pipe -march=native -c -o orf.o orf.c | |
| /gsc/btl/linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Os -w -pipe -march=native -c -o parameters.o parameters.c | |
| /gsc/btl/linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Os -w -pipe -march=native -c -o prob.o prob.c | |
| /gsc/btl/linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Os -w -pipe -march=native -c -o translate.o translate.c | |
| /gsc/btl/linuxbrew/bin/gcc-5 -DHAVE_CONFIG_H -I. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Os -w -pipe -march=native -c -o museq.o museq.c | |
| rm -f libdialign.a | |
| ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o | |
| ranlib libdialign.a | |
| /gsc/btl/linuxbrew/bin/gcc-5 -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o dialign museq.o libdialign.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/dialign' | |
| Making all in Align | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Align' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc | |
| rm -f libalign.a | |
| ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o | |
| ranlib libalign.a | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Align' | |
| Making all in ABYSS | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/ABYSS' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/ABYSS' | |
| Making all in Parallel | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Parallel' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Parallel' | |
| Making all in Bloom | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Bloom' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Bloom' | |
| Making all in BloomDBG | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/BloomDBG' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/BloomDBG' | |
| Making all in Konnector | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Konnector' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Konnector' | |
| Making all in Consensus | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Consensus' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Consensus' | |
| Making all in DAssembler | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DAssembler' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DAssembler' | |
| Making all in DistanceEst | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DistanceEst' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DistanceEst' | |
| Making all in KAligner | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/KAligner' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/KAligner' | |
| Making all in Layout | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Layout' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Layout' | |
| Making all in LogKmerCount | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/LogKmerCount' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/LogKmerCount' | |
| Making all in Map | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Map' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Map' | |
| Making all in MergePaths | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/MergePaths' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/MergePaths' | |
| Making all in Misc | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Misc' | |
| make[2]: Nothing to be done for 'all'. | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Misc' | |
| Making all in Overlap | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Overlap' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Overlap' | |
| Making all in PairedDBG | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PairedDBG' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o KmerPair.o KmerPair.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc | |
| rm -f libpaireddbg.a | |
| ar cru libpaireddbg.a KmerPair.o | |
| ranlib libpaireddbg.a | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PairedDBG' | |
| Making all in ParseAligns | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/ParseAligns' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/ParseAligns' | |
| Making all in PathOverlap | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PathOverlap' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PathOverlap' | |
| Making all in PopBubbles | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PopBubbles' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PopBubbles' | |
| Making all in Scaffold | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Scaffold' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Scaffold' | |
| Making all in SimpleGraph | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/SimpleGraph' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Wno-strict-aliasing -Os -w -pipe -march=native -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Wno-strict-aliasing -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/SimpleGraph' | |
| Making all in kmerprint | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/kmerprint' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/kmerprint' | |
| Making all in FilterGraph | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/FilterGraph' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/FilterGraph' | |
| Making all in GapFiller | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/GapFiller' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/GapFiller' | |
| Making all in Sealer | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Sealer' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Sealer' | |
| Making all in AdjList | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/AdjList' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Os -w -pipe -march=native -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/AdjList' | |
| Making all in lib/bloomfilter | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/bloomfilter' | |
| make[2]: Nothing to be done for 'all'. | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/bloomfilter' | |
| Making all in lib/rolling-hash | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/rolling-hash' | |
| make[2]: Nothing to be done for 'all'. | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/rolling-hash' | |
| Making all in lib/gtest-1.7.0 | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/gtest-1.7.0' | |
| make[2]: Nothing to be done for 'all'. | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/gtest-1.7.0' | |
| Making all in Unittest | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| make[2]: Nothing to be done for 'all'. | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1' | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1' | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1' |
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| 2016-09-25 13:48:26 -0700 | |
| make | |
| check | |
| Making check in bin | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/bin' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/bin' | |
| Making check in doc | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/doc' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/doc' | |
| Making check in Common | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Common' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Common' | |
| Making check in Graph | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Graph' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Graph' | |
| Making check in DataLayer | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DataLayer' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DataLayer' | |
| Making check in DataBase | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DataBase' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DataBase' | |
| Making check in FMIndex | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/FMIndex' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/FMIndex' | |
| Making check in Assembly | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Assembly' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Assembly' | |
| Making check in dialign | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/dialign' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/dialign' | |
| Making check in Align | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Align' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Align' | |
| Making check in ABYSS | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/ABYSS' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/ABYSS' | |
| Making check in Parallel | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Parallel' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Parallel' | |
| Making check in Bloom | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Bloom' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Bloom' | |
| Making check in BloomDBG | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/BloomDBG' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/BloomDBG' | |
| Making check in Konnector | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Konnector' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Konnector' | |
| Making check in Consensus | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Consensus' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Consensus' | |
| Making check in DAssembler | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DAssembler' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DAssembler' | |
| Making check in DistanceEst | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DistanceEst' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/DistanceEst' | |
| Making check in KAligner | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/KAligner' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/KAligner' | |
| Making check in Layout | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Layout' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Layout' | |
| Making check in LogKmerCount | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/LogKmerCount' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/LogKmerCount' | |
| Making check in Map | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Map' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Map' | |
| Making check in MergePaths | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/MergePaths' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/MergePaths' | |
| Making check in Misc | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Misc' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Misc' | |
| Making check in Overlap | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Overlap' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Overlap' | |
| Making check in PairedDBG | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PairedDBG' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PairedDBG' | |
| Making check in ParseAligns | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/ParseAligns' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/ParseAligns' | |
| Making check in PathOverlap | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PathOverlap' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PathOverlap' | |
| Making check in PopBubbles | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PopBubbles' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/PopBubbles' | |
| Making check in Scaffold | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Scaffold' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Scaffold' | |
| Making check in SimpleGraph | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/SimpleGraph' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/SimpleGraph' | |
| Making check in kmerprint | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/kmerprint' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/kmerprint' | |
| Making check in FilterGraph | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/FilterGraph' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/FilterGraph' | |
| Making check in GapFiller | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/GapFiller' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/GapFiller' | |
| Making check in Sealer | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Sealer' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Sealer' | |
| Making check in AdjList | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/AdjList' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/AdjList' | |
| Making check in lib/bloomfilter | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/bloomfilter' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/bloomfilter' | |
| Making check in lib/rolling-hash | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/rolling-hash' | |
| make[1]: Nothing to be done for 'check'. | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/rolling-hash' | |
| Making check in lib/gtest-1.7.0 | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/gtest-1.7.0' | |
| make libgtest.a libgtest_main.a | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/gtest-1.7.0' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -Os -w -pipe -march=native -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -Os -w -pipe -march=native -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -Os -w -pipe -march=native -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc | |
| rm -f libgtest.a | |
| ar cru libgtest.a src/libgtest_a-gtest-all.o | |
| ranlib libgtest.a | |
| rm -f libgtest_main.a | |
| ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o | |
| ranlib libgtest_main.a | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/gtest-1.7.0' | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/lib/gtest-1.7.0' | |
| Making check in Unittest | |
| make[1]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Common/HistogramTest.o Common/HistogramTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Common/KmerTest.o Common/KmerTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Common/Sequence.o Common/Sequence.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Common/SAM.o Common/SAM.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o Konnector/Konnector_DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o Konnector/Konnector_DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o `test -f 'Graph/ConstrainedBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBFSVisitorTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o `test -f 'Graph/BidirectionalBFSTest.cpp' || echo './'`Graph/BidirectionalBFSTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Graph/graph_AllPathsSearch-AllPathsSearchTest.o `test -f 'Graph/AllPathsSearchTest.cpp' || echo './'`Graph/AllPathsSearchTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Graph/graph_HashGraph-HashGraphTest.o `test -f 'Graph/HashGraphTest.cpp' || echo './'`Graph/HashGraphTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o `test -f 'Graph/ConstrainedBidiBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBidiBFSVisitorTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o Konnector/Konnector_konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../DataLayer -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o DBG/DBG_LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../DataLayer -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o PairedDBG/PairedDBG_LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../DataLayer -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o PairedDBG/PairedDBG_KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../DataLayer -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o PairedDBG/PairedDBG_Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../DataLayer -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o PairedDBG/PairedDBG_BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I../Common -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o BloomDBG/BloomDBG_BloomDBG-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o BloomDBG/RollingHashTest.o BloomDBG/RollingHashTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o BloomDBG/RollingHashIteratorTest.o BloomDBG/RollingHashIteratorTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o BloomDBG/BloomDBG_HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -c -o BloomDBG/BloomDBG_RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o common_sequence Common/Sequence.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o common_histogram Common/HistogramTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o PairedDBG_Dinuc PairedDBG/PairedDBG_Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o common_sam Common/SAM.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o PairedDBG_KmerPair PairedDBG/PairedDBG_KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/BloomDBG_HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o common_stringutil Common/StringUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o common_bitutil Common/BitUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o Konnector_DBGBloom Konnector/Konnector_DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o PairedDBG_BranchRecord PairedDBG/PairedDBG_BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o Konnector_DBGBloomAlgorithms Konnector/Konnector_DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o BloomDBG_RollingBloomDBG BloomDBG/BloomDBG_RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o PairedDBG_LoadAlgorithm PairedDBG/PairedDBG_LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o DBG_LoadAlgorithm DBG/DBG_LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o BloomDBG_BloomDBG BloomDBG/BloomDBG_BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| /gsc/btl/linuxbrew/bin/g++-5 -Wall -Wextra -pthread -Wno-error -fopenmp -Os -w -pipe -march=native -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib -o Konnector_konnector Konnector/Konnector_konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| make check-TESTS | |
| make[2]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| make[3]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| PASS: common_kmer | |
| PASS: common_stringutil | |
| PASS: common_sam | |
| PASS: common_bitutil | |
| PASS: common_sequence | |
| PASS: graph_HashGraph | |
| PASS: common_histogram | |
| FAIL: BloomFilter | |
| PASS: graph_BidirectionalBFS | |
| PASS: Konnector_DBGBloomAlgorithms | |
| PASS: graph_AllPathsSearch | |
| PASS: common_KmerIterator | |
| PASS: Konnector_DBGBloom | |
| PASS: graph_ConstrainedBFSVisitor | |
| PASS: graph_ConstrainedBidiBFSVisitor | |
| PASS: BloomDBG_SpacedSeed | |
| PASS: BloomDBG_MaskedKmer | |
| PASS: PairedDBG_KmerPair | |
| PASS: PairedDBG_Dinuc | |
| PASS: BloomDBG_RollingHash | |
| PASS: BloomDBG_BloomDBG | |
| PASS: Konnector_konnector | |
| PASS: BloomDBG_RollingHashIterator | |
| PASS: graph_ExtendPath | |
| PASS: PairedDBG_BranchRecord | |
| PASS: BloomDBG_RollingBloomDBG | |
| PASS: BloomDBG_HashAgnosticCascadingBloom | |
| PASS: PairedDBG_LoadAlgorithm | |
| PASS: DBG_LoadAlgorithm | |
| make[4]: Entering directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| make[4]: Nothing to be done for 'all'. | |
| make[4]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| ============================================================================ | |
| Testsuite summary for ABySS 2.0.1 | |
| ============================================================================ | |
| # TOTAL: 29 | |
| # PASS: 28 | |
| # SKIP: 0 | |
| # XFAIL: 0 | |
| # FAIL: 1 | |
| # XPASS: 0 | |
| # ERROR: 0 | |
| ============================================================================ | |
| See Unittest/test-suite.log | |
| Please report to abyss-users@bcgsc.ca | |
| ============================================================================ | |
| make[3]: *** [Makefile:1479: test-suite.log] Error 1 | |
| make[3]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| make[2]: *** [Makefile:1587: check-TESTS] Error 2 | |
| make[2]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| make[1]: *** [Makefile:1854: check-am] Error 2 | |
| make[1]: Leaving directory '/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/Unittest' | |
| make: *** [Makefile:447: check-recursive] Error 1 | |
| HOMEBREW_VERSION: 0.9.9 | |
| ORIGIN: https://github.com/Linuxbrew/brew.git | |
| HEAD: 28c79defe0ed12f524998a68f22c19ab058b288f | |
| Last commit: 64 minutes ago | |
| Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core | |
| Core tap HEAD: 600e2df32333a66f21d60437446c68e4716a60c5 | |
| Core tap last commit: 23 hours ago | |
| HOMEBREW_PREFIX: /gsc/btl/linuxbrew | |
| HOMEBREW_REPOSITORY: /gsc/btl/linuxbrew | |
| HOMEBREW_CELLAR: /gsc/btl/linuxbrew/Cellar | |
| HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com | |
| CPU: 32-core 64-bit haswell | |
| Homebrew Ruby: 2.3.0 => /gsc/btl/linuxbrew/Cellar/ruby/2.3.0/bin/ruby | |
| Clang: 3.8 build 0 | |
| Git: 2.8.2 => /gsc/btl/linuxbrew/bin/git | |
| Perl: /gsc/btl/linuxbrew/bin/perl => /gsc/btl/linuxbrew/Cellar/perl/5.24.0_1/bin/perl | |
| Python: /gsc/btl/linuxbrew/bin/python => /gsc/btl/linuxbrew/Cellar/python/2.7.12_1/bin/python2.7 | |
| Ruby: /gsc/btl/linuxbrew/bin/ruby => /gsc/btl/linuxbrew/Cellar/ruby/2.3.0/bin/ruby | |
| Java: 1.8.0_102 | |
| Kernel: Linux 2.6.32-573.8.1.el6.x86_64 x86_64 GNU/Linux | |
| OS: CentOS release 6.7 (Final) | |
| OS glibc: 2.12 | |
| OS gcc: 4.4.7 | |
| Linuxbrew glibc: 2.19 | |
| Linuxbrew gcc: 5.3.0 | |
| Linuxbrew xorg: 20160314 | |
| CC: /gsc/btl/linuxbrew/bin/gcc-5 => /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/bin/gcc-5 | |
| CXX: /gsc/btl/linuxbrew/bin/g++-5 => /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/bin/g++-5 | |
| OBJC: /gsc/btl/linuxbrew/bin/gcc-5 | |
| OBJCXX: /gsc/btl/linuxbrew/bin/g++-5 | |
| CFLAGS: -Os -w -pipe -march=native | |
| CXXFLAGS: -Os -w -pipe -march=native | |
| CPPFLAGS: -isystem/gsc/btl/linuxbrew/include | |
| LDFLAGS: -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib | |
| MAKEFLAGS: -j32 | |
| CMAKE_PREFIX_PATH: /gsc/btl/linuxbrew | |
| PKG_CONFIG_LIBDIR: /gsc/btl/linuxbrew/lib/pkgconfig:/gsc/btl/linuxbrew/share/pkgconfig | |
| PATH: /home/sjackman/bin:/gsc/btl/linuxbrew/bin:/gsc/btl/linuxbrew/sbin:/gsc/btl/linuxbrew/Library/Taps/homebrew/homebrew-bundle/cmd:/gsc/btl/linuxbrew/Library/Homebrew/cask/cmd:/gsc/btl/linuxbrew/Library/Homebrew/shims/scm | |
| CPATH: /gsc/btl/linuxbrew/include | |
| LD_LIBRARY_PATH: /gsc/btl/linuxbrew/Cellar/abyss/2.0.1/lib:/gsc/btl/linuxbrew/Cellar/abyss/2.0.1 | |
| LD_RUN_PATH: /gsc/btl/linuxbrew/lib | |
| LIBRARY_PATH: /gsc/btl/linuxbrew/lib |
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| This file contains any messages produced by compilers while | |
| running configure, to aid debugging if configure makes a mistake. | |
| It was created by ABySS configure 2.0.1, which was | |
| generated by GNU Autoconf 2.69. Invocation command line was | |
| $ ./configure --enable-maxk=160 --prefix=/gsc/btl/linuxbrew/Cellar/abyss/2.0.1 --disable-dependency-tracking | |
| ## --------- ## | |
| ## Platform. ## | |
| ## --------- ## | |
| hostname = gphost02 | |
| uname -m = x86_64 | |
| uname -r = 2.6.32-573.8.1.el6.x86_64 | |
| uname -s = Linux | |
| uname -v = #1 SMP Tue Nov 10 18:01:38 UTC 2015 | |
| /usr/bin/uname -p = unknown | |
| /bin/uname -X = unknown | |
| /bin/arch = x86_64 | |
| /usr/bin/arch -k = unknown | |
| /usr/convex/getsysinfo = unknown | |
| /usr/bin/hostinfo = unknown | |
| /bin/machine = unknown | |
| /usr/bin/oslevel = unknown | |
| /bin/universe = unknown | |
| PATH: /home/sjackman/bin | |
| PATH: /gsc/btl/linuxbrew/bin | |
| PATH: /gsc/btl/linuxbrew/sbin | |
| PATH: /gsc/btl/linuxbrew/Library/Taps/homebrew/homebrew-bundle/cmd | |
| PATH: /gsc/btl/linuxbrew/Library/Homebrew/cask/cmd | |
| PATH: /gsc/btl/linuxbrew/Library/Homebrew/shims/scm | |
| ## ----------- ## | |
| ## Core tests. ## | |
| ## ----------- ## | |
| configure:2872: checking for a BSD-compatible install | |
| configure:2940: result: /gsc/btl/linuxbrew/bin/ginstall -c | |
| configure:2951: checking whether build environment is sane | |
| configure:3006: result: yes | |
| configure:3157: checking for a thread-safe mkdir -p | |
| configure:3196: result: /gsc/btl/linuxbrew/bin/mkdir -p | |
| configure:3203: checking for gawk | |
| configure:3219: found /gsc/btl/linuxbrew/bin/gawk | |
| configure:3230: result: gawk | |
| configure:3241: checking whether make sets $(MAKE) | |
| configure:3263: result: yes | |
| configure:3292: checking whether make supports nested variables | |
| configure:3309: result: yes | |
| configure:3397: checking for gawk | |
| configure:3424: result: gawk | |
| configure:3483: checking for gcc | |
| configure:3510: result: /gsc/btl/linuxbrew/bin/gcc-5 | |
| configure:3739: checking for C compiler version | |
| configure:3748: /gsc/btl/linuxbrew/bin/gcc-5 --version >&5 | |
| gcc-5 (Homebrew gcc 5.3.0 --with-glibc) 5.3.0 | |
| Copyright (C) 2015 Free Software Foundation, Inc. | |
| This is free software; see the source for copying conditions. There is NO | |
| warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. | |
| configure:3759: $? = 0 | |
| configure:3748: /gsc/btl/linuxbrew/bin/gcc-5 -v >&5 | |
| Reading specs from /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/specs | |
| COLLECT_GCC=/gsc/btl/linuxbrew/bin/gcc-5 | |
| COLLECT_LTO_WRAPPER=/gsc/btl/linuxbrew/Cellar/gcc/5.3.0/libexec/gcc/x86_64-unknown-linux-gnu/5.3.0/lto-wrapper | |
| Target: x86_64-unknown-linux-gnu | |
| Configured with: ../configure --with-native-system-header-dir=/gsc/btl/linuxbrew/include --with-build-time-tools=/gsc/btl/linuxbrew/Cellar/binutils/2.25.1/x86_64-unknown-linux-gnu/bin --with-boot-ldflags='-static-libstdc++ -static-libgcc -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/opt/glibc/lib/ld-linux-x86-64.so.2 -Wl,-rpath,/gsc/btl/linuxbrew/lib' --prefix=/gsc/btl/linuxbrew/Cellar/gcc/5.3.0 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-5 --with-gmp=/gsc/btl/linuxbrew/opt/gmp --with-mpfr=/gsc/btl/linuxbrew/opt/mpfr --with-mpc=/gsc/btl/linuxbrew/opt/libmpc --with-isl=/gsc/btl/linuxbrew/opt/isl --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --with-build-config=bootstrap-debug --disable-werror --with-pkgversion='Homebrew gcc 5.3.0 --with-glibc' --with-bugurl=https://github.com/Homebrew/homebrew/issues --enable-plugin --disable-nls --disable-multilib | |
| Thread model: posix | |
| gcc version 5.3.0 (Homebrew gcc 5.3.0 --with-glibc) | |
| configure:3759: $? = 0 | |
| configure:3748: /gsc/btl/linuxbrew/bin/gcc-5 -V >&5 | |
| gcc-5: error: unrecognized command line option '-V' | |
| gcc-5: fatal error: no input files | |
| compilation terminated. | |
| configure:3759: $? = 1 | |
| configure:3748: /gsc/btl/linuxbrew/bin/gcc-5 -qversion >&5 | |
| gcc-5: error: unrecognized command line option '-qversion' | |
| gcc-5: fatal error: no input files | |
| compilation terminated. | |
| configure:3759: $? = 1 | |
| configure:3779: checking whether the C compiler works | |
| configure:3801: /gsc/btl/linuxbrew/bin/gcc-5 -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:3805: $? = 0 | |
| configure:3853: result: yes | |
| configure:3856: checking for C compiler default output file name | |
| configure:3858: result: a.out | |
| configure:3864: checking for suffix of executables | |
| configure:3871: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:3875: $? = 0 | |
| configure:3897: result: | |
| configure:3919: checking whether we are cross compiling | |
| configure:3927: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:3931: $? = 0 | |
| configure:3938: ./conftest | |
| configure:3942: $? = 0 | |
| configure:3957: result: no | |
| configure:3962: checking for suffix of object files | |
| configure:3984: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:3988: $? = 0 | |
| configure:4009: result: o | |
| configure:4013: checking whether we are using the GNU C compiler | |
| configure:4032: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:4032: $? = 0 | |
| configure:4041: result: yes | |
| configure:4050: checking whether /gsc/btl/linuxbrew/bin/gcc-5 accepts -g | |
| configure:4070: /gsc/btl/linuxbrew/bin/gcc-5 -c -g -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:4070: $? = 0 | |
| configure:4111: result: yes | |
| configure:4128: checking for /gsc/btl/linuxbrew/bin/gcc-5 option to accept ISO C89 | |
| configure:4191: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:4191: $? = 0 | |
| configure:4204: result: none needed | |
| configure:4235: checking for style of include used by make | |
| configure:4263: result: GNU | |
| configure:4289: checking dependency style of /gsc/btl/linuxbrew/bin/gcc-5 | |
| configure:4400: result: none | |
| configure:4420: checking how to run the C preprocessor | |
| configure:4451: /gsc/btl/linuxbrew/bin/gcc-5 -E -isystem/gsc/btl/linuxbrew/include conftest.c | |
| configure:4451: $? = 0 | |
| configure:4465: /gsc/btl/linuxbrew/bin/gcc-5 -E -isystem/gsc/btl/linuxbrew/include conftest.c | |
| conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory | |
| compilation terminated. | |
| configure:4465: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | /* end confdefs.h. */ | |
| | #include <ac_nonexistent.h> | |
| configure:4490: result: /gsc/btl/linuxbrew/bin/gcc-5 -E | |
| configure:4510: /gsc/btl/linuxbrew/bin/gcc-5 -E -isystem/gsc/btl/linuxbrew/include conftest.c | |
| configure:4510: $? = 0 | |
| configure:4524: /gsc/btl/linuxbrew/bin/gcc-5 -E -isystem/gsc/btl/linuxbrew/include conftest.c | |
| conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory | |
| compilation terminated. | |
| configure:4524: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | /* end confdefs.h. */ | |
| | #include <ac_nonexistent.h> | |
| configure:4664: checking for C++ compiler version | |
| configure:4673: /gsc/btl/linuxbrew/bin/g++-5 --version >&5 | |
| g++-5 (Homebrew gcc 5.3.0 --with-glibc) 5.3.0 | |
| Copyright (C) 2015 Free Software Foundation, Inc. | |
| This is free software; see the source for copying conditions. There is NO | |
| warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. | |
| configure:4684: $? = 0 | |
| configure:4673: /gsc/btl/linuxbrew/bin/g++-5 -v >&5 | |
| Reading specs from /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/specs | |
| COLLECT_GCC=/gsc/btl/linuxbrew/bin/g++-5 | |
| COLLECT_LTO_WRAPPER=/gsc/btl/linuxbrew/Cellar/gcc/5.3.0/libexec/gcc/x86_64-unknown-linux-gnu/5.3.0/lto-wrapper | |
| Target: x86_64-unknown-linux-gnu | |
| Configured with: ../configure --with-native-system-header-dir=/gsc/btl/linuxbrew/include --with-build-time-tools=/gsc/btl/linuxbrew/Cellar/binutils/2.25.1/x86_64-unknown-linux-gnu/bin --with-boot-ldflags='-static-libstdc++ -static-libgcc -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/opt/glibc/lib/ld-linux-x86-64.so.2 -Wl,-rpath,/gsc/btl/linuxbrew/lib' --prefix=/gsc/btl/linuxbrew/Cellar/gcc/5.3.0 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-5 --with-gmp=/gsc/btl/linuxbrew/opt/gmp --with-mpfr=/gsc/btl/linuxbrew/opt/mpfr --with-mpc=/gsc/btl/linuxbrew/opt/libmpc --with-isl=/gsc/btl/linuxbrew/opt/isl --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --with-build-config=bootstrap-debug --disable-werror --with-pkgversion='Homebrew gcc 5.3.0 --with-glibc' --with-bugurl=https://github.com/Homebrew/homebrew/issues --enable-plugin --disable-nls --disable-multilib | |
| Thread model: posix | |
| gcc version 5.3.0 (Homebrew gcc 5.3.0 --with-glibc) | |
| configure:4684: $? = 0 | |
| configure:4673: /gsc/btl/linuxbrew/bin/g++-5 -V >&5 | |
| g++-5: error: unrecognized command line option '-V' | |
| g++-5: fatal error: no input files | |
| compilation terminated. | |
| configure:4684: $? = 1 | |
| configure:4673: /gsc/btl/linuxbrew/bin/g++-5 -qversion >&5 | |
| g++-5: error: unrecognized command line option '-qversion' | |
| g++-5: fatal error: no input files | |
| compilation terminated. | |
| configure:4684: $? = 1 | |
| configure:4688: checking whether we are using the GNU C++ compiler | |
| configure:4707: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.cpp >&5 | |
| configure:4707: $? = 0 | |
| configure:4716: result: yes | |
| configure:4725: checking whether /gsc/btl/linuxbrew/bin/g++-5 accepts -g | |
| configure:4745: /gsc/btl/linuxbrew/bin/g++-5 -c -g -isystem/gsc/btl/linuxbrew/include conftest.cpp >&5 | |
| configure:4745: $? = 0 | |
| configure:4786: result: yes | |
| configure:4811: checking dependency style of /gsc/btl/linuxbrew/bin/g++-5 | |
| configure:4922: result: none | |
| configure:4981: checking for ranlib | |
| configure:4997: found /gsc/btl/linuxbrew/bin/ranlib | |
| configure:5008: result: ranlib | |
| configure:5073: checking for ghc | |
| configure:5089: found /gsc/btl/linuxbrew/bin/ghc | |
| configure:5100: result: ghc | |
| configure:5165: checking for ghc-pkg | |
| configure:5181: found /gsc/btl/linuxbrew/bin/ghc-pkg | |
| configure:5192: result: ghc-pkg | |
| configure:5224: checking for pandoc | |
| configure:5240: found /gsc/btl/linuxbrew/bin/pandoc | |
| configure:5251: result: yes | |
| configure:5271: checking for grep that handles long lines and -e | |
| configure:5329: result: /gsc/btl/linuxbrew/bin/grep | |
| configure:5334: checking for egrep | |
| configure:5396: result: /gsc/btl/linuxbrew/bin/grep -E | |
| configure:5401: checking for ANSI C header files | |
| configure:5421: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5421: $? = 0 | |
| configure:5494: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:5494: $? = 0 | |
| configure:5494: ./conftest | |
| configure:5494: $? = 0 | |
| configure:5505: result: yes | |
| configure:5518: checking for sys/types.h | |
| configure:5518: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5518: $? = 0 | |
| configure:5518: result: yes | |
| configure:5518: checking for sys/stat.h | |
| configure:5518: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5518: $? = 0 | |
| configure:5518: result: yes | |
| configure:5518: checking for stdlib.h | |
| configure:5518: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5518: $? = 0 | |
| configure:5518: result: yes | |
| configure:5518: checking for string.h | |
| configure:5518: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5518: $? = 0 | |
| configure:5518: result: yes | |
| configure:5518: checking for memory.h | |
| configure:5518: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5518: $? = 0 | |
| configure:5518: result: yes | |
| configure:5518: checking for strings.h | |
| configure:5518: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5518: $? = 0 | |
| configure:5518: result: yes | |
| configure:5518: checking for inttypes.h | |
| configure:5518: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5518: $? = 0 | |
| configure:5518: result: yes | |
| configure:5518: checking for stdint.h | |
| configure:5518: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5518: $? = 0 | |
| configure:5518: result: yes | |
| configure:5518: checking for unistd.h | |
| configure:5518: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5518: $? = 0 | |
| configure:5518: result: yes | |
| configure:5534: checking dlfcn.h usability | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking dlfcn.h presence | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -E -isystem/gsc/btl/linuxbrew/include conftest.c | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking for dlfcn.h | |
| configure:5534: result: yes | |
| configure:5534: checking fcntl.h usability | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking fcntl.h presence | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -E -isystem/gsc/btl/linuxbrew/include conftest.c | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking for fcntl.h | |
| configure:5534: result: yes | |
| configure:5534: checking float.h usability | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking float.h presence | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -E -isystem/gsc/btl/linuxbrew/include conftest.c | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking for float.h | |
| configure:5534: result: yes | |
| configure:5534: checking limits.h usability | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking limits.h presence | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -E -isystem/gsc/btl/linuxbrew/include conftest.c | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking for limits.h | |
| configure:5534: result: yes | |
| configure:5534: checking stddef.h usability | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking stddef.h presence | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -E -isystem/gsc/btl/linuxbrew/include conftest.c | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking for stddef.h | |
| configure:5534: result: yes | |
| configure:5534: checking for stdint.h | |
| configure:5534: result: yes | |
| configure:5534: checking for stdlib.h | |
| configure:5534: result: yes | |
| configure:5534: checking sys/param.h usability | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking sys/param.h presence | |
| configure:5534: /gsc/btl/linuxbrew/bin/gcc-5 -E -isystem/gsc/btl/linuxbrew/include conftest.c | |
| configure:5534: $? = 0 | |
| configure:5534: result: yes | |
| configure:5534: checking for sys/param.h | |
| configure:5534: result: yes | |
| configure:5544: checking for stdbool.h that conforms to C99 | |
| configure:5611: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5611: $? = 0 | |
| configure:5618: result: yes | |
| configure:5620: checking for _Bool | |
| configure:5620: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5620: $? = 0 | |
| configure:5620: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:65:20: error: expected expression before ')' token | |
| if (sizeof ((_Bool))) | |
| ^ | |
| configure:5620: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | /* end confdefs.h. */ | |
| | #include <stdio.h> | |
| | #ifdef HAVE_SYS_TYPES_H | |
| | # include <sys/types.h> | |
| | #endif | |
| | #ifdef HAVE_SYS_STAT_H | |
| | # include <sys/stat.h> | |
| | #endif | |
| | #ifdef STDC_HEADERS | |
| | # include <stdlib.h> | |
| | # include <stddef.h> | |
| | #else | |
| | # ifdef HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | # endif | |
| | #endif | |
| | #ifdef HAVE_STRING_H | |
| | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | |
| | # include <memory.h> | |
| | # endif | |
| | # include <string.h> | |
| | #endif | |
| | #ifdef HAVE_STRINGS_H | |
| | # include <strings.h> | |
| | #endif | |
| | #ifdef HAVE_INTTYPES_H | |
| | # include <inttypes.h> | |
| | #endif | |
| | #ifdef HAVE_STDINT_H | |
| | # include <stdint.h> | |
| | #endif | |
| | #ifdef HAVE_UNISTD_H | |
| | # include <unistd.h> | |
| | #endif | |
| | int | |
| | main () | |
| | { | |
| | if (sizeof ((_Bool))) | |
| | return 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:5620: result: yes | |
| configure:5637: checking for ANSI C header files | |
| configure:5741: result: yes | |
| configure:5751: checking whether byte ordering is bigendian | |
| configure:5766: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| conftest.c:33:9: error: unknown type name 'not' | |
| not a universal capable compiler | |
| ^ | |
| conftest.c:33:15: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'universal' | |
| not a universal capable compiler | |
| ^ | |
| conftest.c:33:15: error: unknown type name 'universal' | |
| configure:5766: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | /* end confdefs.h. */ | |
| | #ifndef __APPLE_CC__ | |
| | not a universal capable compiler | |
| | #endif | |
| | typedef int dummy; | |
| | | |
| configure:5811: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:5811: $? = 0 | |
| configure:5829: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:39:4: error: unknown type name 'not' | |
| not big endian | |
| ^ | |
| conftest.c:39:12: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'endian' | |
| not big endian | |
| ^ | |
| configure:5829: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | /* end confdefs.h. */ | |
| | #include <sys/types.h> | |
| | #include <sys/param.h> | |
| | | |
| | int | |
| | main () | |
| | { | |
| | #if BYTE_ORDER != BIG_ENDIAN | |
| | not big endian | |
| | #endif | |
| | | |
| | ; | |
| | return 0; | |
| | } | |
| configure:5957: result: no | |
| configure:5975: checking for an ANSI C-conforming const | |
| configure:6041: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6041: $? = 0 | |
| configure:6048: result: yes | |
| configure:6056: checking for inline | |
| configure:6072: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6072: $? = 0 | |
| configure:6080: result: inline | |
| configure:6098: checking for ptrdiff_t | |
| configure:6098: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6098: $? = 0 | |
| configure:6098: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:68:24: error: expected expression before ')' token | |
| if (sizeof ((ptrdiff_t))) | |
| ^ | |
| configure:6098: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | /* end confdefs.h. */ | |
| | #include <stdio.h> | |
| | #ifdef HAVE_SYS_TYPES_H | |
| | # include <sys/types.h> | |
| | #endif | |
| | #ifdef HAVE_SYS_STAT_H | |
| | # include <sys/stat.h> | |
| | #endif | |
| | #ifdef STDC_HEADERS | |
| | # include <stdlib.h> | |
| | # include <stddef.h> | |
| | #else | |
| | # ifdef HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | # endif | |
| | #endif | |
| | #ifdef HAVE_STRING_H | |
| | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | |
| | # include <memory.h> | |
| | # endif | |
| | # include <string.h> | |
| | #endif | |
| | #ifdef HAVE_STRINGS_H | |
| | # include <strings.h> | |
| | #endif | |
| | #ifdef HAVE_INTTYPES_H | |
| | # include <inttypes.h> | |
| | #endif | |
| | #ifdef HAVE_STDINT_H | |
| | # include <stdint.h> | |
| | #endif | |
| | #ifdef HAVE_UNISTD_H | |
| | # include <unistd.h> | |
| | #endif | |
| | int | |
| | main () | |
| | { | |
| | if (sizeof ((ptrdiff_t))) | |
| | return 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6098: result: yes | |
| configure:6108: checking for mode_t | |
| configure:6108: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6108: $? = 0 | |
| configure:6108: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:69:21: error: expected expression before ')' token | |
| if (sizeof ((mode_t))) | |
| ^ | |
| configure:6108: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | /* end confdefs.h. */ | |
| | #include <stdio.h> | |
| | #ifdef HAVE_SYS_TYPES_H | |
| | # include <sys/types.h> | |
| | #endif | |
| | #ifdef HAVE_SYS_STAT_H | |
| | # include <sys/stat.h> | |
| | #endif | |
| | #ifdef STDC_HEADERS | |
| | # include <stdlib.h> | |
| | # include <stddef.h> | |
| | #else | |
| | # ifdef HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | # endif | |
| | #endif | |
| | #ifdef HAVE_STRING_H | |
| | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | |
| | # include <memory.h> | |
| | # endif | |
| | # include <string.h> | |
| | #endif | |
| | #ifdef HAVE_STRINGS_H | |
| | # include <strings.h> | |
| | #endif | |
| | #ifdef HAVE_INTTYPES_H | |
| | # include <inttypes.h> | |
| | #endif | |
| | #ifdef HAVE_STDINT_H | |
| | # include <stdint.h> | |
| | #endif | |
| | #ifdef HAVE_UNISTD_H | |
| | # include <unistd.h> | |
| | #endif | |
| | int | |
| | main () | |
| | { | |
| | if (sizeof ((mode_t))) | |
| | return 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6108: result: yes | |
| configure:6119: checking for pid_t | |
| configure:6119: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6119: $? = 0 | |
| configure:6119: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:69:20: error: expected expression before ')' token | |
| if (sizeof ((pid_t))) | |
| ^ | |
| configure:6119: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | /* end confdefs.h. */ | |
| | #include <stdio.h> | |
| | #ifdef HAVE_SYS_TYPES_H | |
| | # include <sys/types.h> | |
| | #endif | |
| | #ifdef HAVE_SYS_STAT_H | |
| | # include <sys/stat.h> | |
| | #endif | |
| | #ifdef STDC_HEADERS | |
| | # include <stdlib.h> | |
| | # include <stddef.h> | |
| | #else | |
| | # ifdef HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | # endif | |
| | #endif | |
| | #ifdef HAVE_STRING_H | |
| | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | |
| | # include <memory.h> | |
| | # endif | |
| | # include <string.h> | |
| | #endif | |
| | #ifdef HAVE_STRINGS_H | |
| | # include <strings.h> | |
| | #endif | |
| | #ifdef HAVE_INTTYPES_H | |
| | # include <inttypes.h> | |
| | #endif | |
| | #ifdef HAVE_STDINT_H | |
| | # include <stdint.h> | |
| | #endif | |
| | #ifdef HAVE_UNISTD_H | |
| | # include <unistd.h> | |
| | #endif | |
| | int | |
| | main () | |
| | { | |
| | if (sizeof ((pid_t))) | |
| | return 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6119: result: yes | |
| configure:6130: checking for size_t | |
| configure:6130: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6130: $? = 0 | |
| configure:6130: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:69:21: error: expected expression before ')' token | |
| if (sizeof ((size_t))) | |
| ^ | |
| configure:6130: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | /* end confdefs.h. */ | |
| | #include <stdio.h> | |
| | #ifdef HAVE_SYS_TYPES_H | |
| | # include <sys/types.h> | |
| | #endif | |
| | #ifdef HAVE_SYS_STAT_H | |
| | # include <sys/stat.h> | |
| | #endif | |
| | #ifdef STDC_HEADERS | |
| | # include <stdlib.h> | |
| | # include <stddef.h> | |
| | #else | |
| | # ifdef HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | # endif | |
| | #endif | |
| | #ifdef HAVE_STRING_H | |
| | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | |
| | # include <memory.h> | |
| | # endif | |
| | # include <string.h> | |
| | #endif | |
| | #ifdef HAVE_STRINGS_H | |
| | # include <strings.h> | |
| | #endif | |
| | #ifdef HAVE_INTTYPES_H | |
| | # include <inttypes.h> | |
| | #endif | |
| | #ifdef HAVE_STDINT_H | |
| | # include <stdint.h> | |
| | #endif | |
| | #ifdef HAVE_UNISTD_H | |
| | # include <unistd.h> | |
| | #endif | |
| | int | |
| | main () | |
| | { | |
| | if (sizeof ((size_t))) | |
| | return 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6130: result: yes | |
| configure:6141: checking for ssize_t | |
| configure:6141: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6141: $? = 0 | |
| configure:6141: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:69:22: error: expected expression before ')' token | |
| if (sizeof ((ssize_t))) | |
| ^ | |
| configure:6141: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | /* end confdefs.h. */ | |
| | #include <stdio.h> | |
| | #ifdef HAVE_SYS_TYPES_H | |
| | # include <sys/types.h> | |
| | #endif | |
| | #ifdef HAVE_SYS_STAT_H | |
| | # include <sys/stat.h> | |
| | #endif | |
| | #ifdef STDC_HEADERS | |
| | # include <stdlib.h> | |
| | # include <stddef.h> | |
| | #else | |
| | # ifdef HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | # endif | |
| | #endif | |
| | #ifdef HAVE_STRING_H | |
| | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | |
| | # include <memory.h> | |
| | # endif | |
| | # include <string.h> | |
| | #endif | |
| | #ifdef HAVE_STRINGS_H | |
| | # include <strings.h> | |
| | #endif | |
| | #ifdef HAVE_INTTYPES_H | |
| | # include <inttypes.h> | |
| | #endif | |
| | #ifdef HAVE_STDINT_H | |
| | # include <stdint.h> | |
| | #endif | |
| | #ifdef HAVE_UNISTD_H | |
| | # include <unistd.h> | |
| | #endif | |
| | int | |
| | main () | |
| | { | |
| | if (sizeof ((ssize_t))) | |
| | return 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6141: result: yes | |
| configure:6152: checking for int64_t | |
| configure:6152: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6152: $? = 0 | |
| configure:6152: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| conftest.c: In function 'main': | |
| conftest.c:70:12: error: storage size of 'test_array' isn't constant | |
| static int test_array [1 - 2 * !((int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 1) | |
| ^ | |
| configure:6152: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | /* end confdefs.h. */ | |
| | #include <stdio.h> | |
| | #ifdef HAVE_SYS_TYPES_H | |
| | # include <sys/types.h> | |
| | #endif | |
| | #ifdef HAVE_SYS_STAT_H | |
| | # include <sys/stat.h> | |
| | #endif | |
| | #ifdef STDC_HEADERS | |
| | # include <stdlib.h> | |
| | # include <stddef.h> | |
| | #else | |
| | # ifdef HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | # endif | |
| | #endif | |
| | #ifdef HAVE_STRING_H | |
| | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | |
| | # include <memory.h> | |
| | # endif | |
| | # include <string.h> | |
| | #endif | |
| | #ifdef HAVE_STRINGS_H | |
| | # include <strings.h> | |
| | #endif | |
| | #ifdef HAVE_INTTYPES_H | |
| | # include <inttypes.h> | |
| | #endif | |
| | #ifdef HAVE_STDINT_H | |
| | # include <stdint.h> | |
| | #endif | |
| | #ifdef HAVE_UNISTD_H | |
| | # include <unistd.h> | |
| | #endif | |
| | enum { N = 64 / 2 - 1 }; | |
| | int | |
| | main () | |
| | { | |
| | static int test_array [1 - 2 * !((int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 1) | |
| | < (int64_t) (((((int64_t) 1 << N) << N) - 1) * 2 + 2))]; | |
| | test_array [0] = 0; | |
| | return test_array [0]; | |
| | | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6152: result: yes | |
| configure:6163: checking for uint8_t | |
| configure:6163: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6163: $? = 0 | |
| configure:6163: result: yes | |
| configure:6177: checking for uint16_t | |
| configure:6177: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6177: $? = 0 | |
| configure:6177: result: yes | |
| configure:6189: checking for uint32_t | |
| configure:6189: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6189: $? = 0 | |
| configure:6189: result: yes | |
| configure:6203: checking for uint64_t | |
| configure:6203: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6203: $? = 0 | |
| configure:6203: result: yes | |
| configure:6227: checking for std::hash<int> | |
| configure:6227: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.cpp >&5 | |
| conftest.cpp: In function 'int main()': | |
| conftest.cpp:43:13: error: 'hash' is not a member of 'std' | |
| if (sizeof (std::hash<int>)) | |
| ^ | |
| conftest.cpp:43:23: error: expected primary-expression before 'int' | |
| if (sizeof (std::hash<int>)) | |
| ^ | |
| conftest.cpp:43:23: error: expected ')' before 'int' | |
| conftest.cpp:44:11: error: expected ')' before ';' token | |
| return 0; | |
| ^ | |
| configure:6227: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | /* end confdefs.h. */ | |
| | | |
| | #ifdef __FUJITSU | |
| | #include <string> | |
| | #else | |
| | #include <functional> | |
| | #endif | |
| | | |
| | int | |
| | main () | |
| | { | |
| | if (sizeof (std::hash<int>)) | |
| | return 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6227: result: no | |
| configure:6241: checking for std::tr1::hash<int> | |
| configure:6241: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.cpp >&5 | |
| configure:6241: $? = 0 | |
| configure:6241: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.cpp >&5 | |
| conftest.cpp: In function 'int main()': | |
| conftest.cpp:38:33: error: expected primary-expression before ')' token | |
| if (sizeof ((std::tr1::hash<int>))) | |
| ^ | |
| configure:6241: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | /* end confdefs.h. */ | |
| | #include <tr1/functional> | |
| | | |
| | int | |
| | main () | |
| | { | |
| | if (sizeof ((std::tr1::hash<int>))) | |
| | return 0; | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6241: result: yes | |
| configure:6261: checking for dup2 | |
| configure:6261: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6261: $? = 0 | |
| configure:6261: result: yes | |
| configure:6261: checking for gethostname | |
| configure:6261: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6261: $? = 0 | |
| configure:6261: result: yes | |
| configure:6261: checking for getopt_long | |
| configure:6261: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6261: $? = 0 | |
| configure:6261: result: yes | |
| configure:6261: checking for getpagesize | |
| configure:6261: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6261: $? = 0 | |
| configure:6261: result: yes | |
| configure:6261: checking for memset | |
| configure:6261: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6261: $? = 0 | |
| configure:6261: result: yes | |
| configure:6261: checking for strdup | |
| configure:6261: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6261: $? = 0 | |
| configure:6261: result: yes | |
| configure:6261: checking for strerror | |
| configure:6261: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6261: $? = 0 | |
| configure:6261: result: yes | |
| configure:6261: checking for strtoul | |
| configure:6261: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6261: $? = 0 | |
| configure:6261: result: yes | |
| configure:6272: checking vfork.h usability | |
| configure:6272: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| conftest.c:75:19: fatal error: vfork.h: No such file or directory | |
| compilation terminated. | |
| configure:6272: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | /* end confdefs.h. */ | |
| | #include <stdio.h> | |
| | #ifdef HAVE_SYS_TYPES_H | |
| | # include <sys/types.h> | |
| | #endif | |
| | #ifdef HAVE_SYS_STAT_H | |
| | # include <sys/stat.h> | |
| | #endif | |
| | #ifdef STDC_HEADERS | |
| | # include <stdlib.h> | |
| | # include <stddef.h> | |
| | #else | |
| | # ifdef HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | # endif | |
| | #endif | |
| | #ifdef HAVE_STRING_H | |
| | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | |
| | # include <memory.h> | |
| | # endif | |
| | # include <string.h> | |
| | #endif | |
| | #ifdef HAVE_STRINGS_H | |
| | # include <strings.h> | |
| | #endif | |
| | #ifdef HAVE_INTTYPES_H | |
| | # include <inttypes.h> | |
| | #endif | |
| | #ifdef HAVE_STDINT_H | |
| | # include <stdint.h> | |
| | #endif | |
| | #ifdef HAVE_UNISTD_H | |
| | # include <unistd.h> | |
| | #endif | |
| | #include <vfork.h> | |
| configure:6272: result: no | |
| configure:6272: checking vfork.h presence | |
| configure:6272: /gsc/btl/linuxbrew/bin/gcc-5 -E -isystem/gsc/btl/linuxbrew/include conftest.c | |
| conftest.c:42:19: fatal error: vfork.h: No such file or directory | |
| compilation terminated. | |
| configure:6272: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | /* end confdefs.h. */ | |
| | #include <vfork.h> | |
| configure:6272: result: no | |
| configure:6272: checking for vfork.h | |
| configure:6272: result: no | |
| configure:6285: checking for fork | |
| configure:6285: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6285: $? = 0 | |
| configure:6285: result: yes | |
| configure:6285: checking for vfork | |
| configure:6285: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6285: $? = 0 | |
| configure:6285: result: yes | |
| configure:6295: checking for working fork | |
| configure:6317: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6317: $? = 0 | |
| configure:6317: ./conftest | |
| configure:6317: $? = 0 | |
| configure:6327: result: yes | |
| configure:6348: checking for working vfork | |
| configure:6458: result: yes | |
| configure:6485: checking for stdlib.h | |
| configure:6485: result: yes | |
| configure:6495: checking for GNU libc compatible malloc | |
| configure:6519: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6519: $? = 0 | |
| configure:6519: ./conftest | |
| configure:6519: $? = 0 | |
| configure:6529: result: yes | |
| configure:6550: checking for working memcmp | |
| configure:6593: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6593: $? = 0 | |
| configure:6593: ./conftest | |
| configure:6593: $? = 0 | |
| configure:6603: result: yes | |
| configure:6614: checking for stdlib.h | |
| configure:6614: result: yes | |
| configure:6624: checking for GNU libc compatible realloc | |
| configure:6648: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6648: $? = 0 | |
| configure:6648: ./conftest | |
| configure:6648: $? = 0 | |
| configure:6658: result: yes | |
| configure:6688: checking for vprintf | |
| configure:6688: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:6688: $? = 0 | |
| configure:6688: result: yes | |
| configure:6694: checking for _doprnt | |
| configure:6694: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| /var/tmp/sjackman/ccZFpPVI.o: In function `main': | |
| conftest.c:(.text.startup+0x4): undefined reference to `_doprnt' | |
| collect2: error: ld returned 1 exit status | |
| configure:6694: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | /* end confdefs.h. */ | |
| | /* Define _doprnt to an innocuous variant, in case <limits.h> declares _doprnt. | |
| | For example, HP-UX 11i <limits.h> declares gettimeofday. */ | |
| | #define _doprnt innocuous__doprnt | |
| | | |
| | /* System header to define __stub macros and hopefully few prototypes, | |
| | which can conflict with char _doprnt (); below. | |
| | Prefer <limits.h> to <assert.h> if __STDC__ is defined, since | |
| | <limits.h> exists even on freestanding compilers. */ | |
| | | |
| | #ifdef __STDC__ | |
| | # include <limits.h> | |
| | #else | |
| | # include <assert.h> | |
| | #endif | |
| | | |
| | #undef _doprnt | |
| | | |
| | /* Override any GCC internal prototype to avoid an error. | |
| | Use char because int might match the return type of a GCC | |
| | builtin and then its argument prototype would still apply. */ | |
| | #ifdef __cplusplus | |
| | extern "C" | |
| | #endif | |
| | char _doprnt (); | |
| | /* The GNU C library defines this for functions which it implements | |
| | to always fail with ENOSYS. Some functions are actually named | |
| | something starting with __ and the normal name is an alias. */ | |
| | #if defined __stub__doprnt || defined __stub____doprnt | |
| | choke me | |
| | #endif | |
| | | |
| | int | |
| | main () | |
| | { | |
| | return _doprnt (); | |
| | ; | |
| | return 0; | |
| | } | |
| configure:6694: result: no | |
| configure:6707: checking whether HOST_NAME_MAX is declared | |
| configure:6707: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -isystem/gsc/btl/linuxbrew/include conftest.c >&5 | |
| configure:6707: $? = 0 | |
| configure:6707: result: yes | |
| configure:6841: checking build system type | |
| configure:6855: result: x86_64-unknown-linux-gnu | |
| configure:6875: checking host system type | |
| configure:6888: result: x86_64-unknown-linux-gnu | |
| configure:7020: checking if compiler needs -Werror to reject unknown flags | |
| configure:7036: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -Werror -Wunknown-warning-option -Wsizeof-array-argument -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.c >&5 | |
| gcc-5: error: unrecognized command line option '-Wunknown-warning-option' | |
| configure:7036: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | /* end confdefs.h. */ | |
| | int foo(void); | |
| | int | |
| | main () | |
| | { | |
| | foo() | |
| | ; | |
| | return 0; | |
| | } | |
| configure:7041: result: no | |
| configure:7107: checking for the pthreads library -lpthreads | |
| configure:7145: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c -lpthreads >&5 | |
| /gsc/btl/linuxbrew/bin/ld: cannot find -lpthreads | |
| collect2: error: ld returned 1 exit status | |
| configure:7145: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | /* end confdefs.h. */ | |
| | #include <pthread.h> | |
| | static void routine(void *a) { a = 0; } | |
| | static void *start_routine(void *a) { return a; } | |
| | int | |
| | main () | |
| | { | |
| | pthread_t th; pthread_attr_t attr; | |
| | pthread_create(&th, 0, start_routine, 0); | |
| | pthread_join(th, 0); | |
| | pthread_attr_init(&attr); | |
| | pthread_cleanup_push(routine, 0); | |
| | pthread_cleanup_pop(0) /* ; */ | |
| | ; | |
| | return 0; | |
| | } | |
| configure:7154: result: no | |
| configure:7052: checking whether pthreads work without any flags | |
| configure:7145: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| /var/tmp/sjackman/ccrOdA7c.o: In function `main': | |
| conftest.c:(.text.startup+0x14): undefined reference to `pthread_create' | |
| conftest.c:(.text.startup+0x1f): undefined reference to `pthread_join' | |
| conftest.c:(.text.startup+0x54): undefined reference to `__pthread_register_cancel' | |
| conftest.c:(.text.startup+0x5e): undefined reference to `__pthread_unregister_cancel' | |
| collect2: error: ld returned 1 exit status | |
| configure:7145: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | /* end confdefs.h. */ | |
| | #include <pthread.h> | |
| | static void routine(void *a) { a = 0; } | |
| | static void *start_routine(void *a) { return a; } | |
| | int | |
| | main () | |
| | { | |
| | pthread_t th; pthread_attr_t attr; | |
| | pthread_create(&th, 0, start_routine, 0); | |
| | pthread_join(th, 0); | |
| | pthread_attr_init(&attr); | |
| | pthread_cleanup_push(routine, 0); | |
| | pthread_cleanup_pop(0) /* ; */ | |
| | ; | |
| | return 0; | |
| | } | |
| configure:7154: result: no | |
| configure:7057: checking whether pthreads work with -Kthread | |
| configure:7145: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -Kthread -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| gcc-5: error: unrecognized command line option '-Kthread' | |
| configure:7145: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | /* end confdefs.h. */ | |
| | #include <pthread.h> | |
| | static void routine(void *a) { a = 0; } | |
| | static void *start_routine(void *a) { return a; } | |
| | int | |
| | main () | |
| | { | |
| | pthread_t th; pthread_attr_t attr; | |
| | pthread_create(&th, 0, start_routine, 0); | |
| | pthread_join(th, 0); | |
| | pthread_attr_init(&attr); | |
| | pthread_cleanup_push(routine, 0); | |
| | pthread_cleanup_pop(0) /* ; */ | |
| | ; | |
| | return 0; | |
| | } | |
| configure:7154: result: no | |
| configure:7057: checking whether pthreads work with -kthread | |
| configure:7145: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -kthread -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| gcc-5: error: unrecognized command line option '-kthread' | |
| configure:7145: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | /* end confdefs.h. */ | |
| | #include <pthread.h> | |
| | static void routine(void *a) { a = 0; } | |
| | static void *start_routine(void *a) { return a; } | |
| | int | |
| | main () | |
| | { | |
| | pthread_t th; pthread_attr_t attr; | |
| | pthread_create(&th, 0, start_routine, 0); | |
| | pthread_join(th, 0); | |
| | pthread_attr_init(&attr); | |
| | pthread_cleanup_push(routine, 0); | |
| | pthread_cleanup_pop(0) /* ; */ | |
| | ; | |
| | return 0; | |
| | } | |
| configure:7154: result: no | |
| configure:7107: checking for the pthreads library -llthread | |
| configure:7145: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c -llthread >&5 | |
| /gsc/btl/linuxbrew/bin/ld: cannot find -llthread | |
| collect2: error: ld returned 1 exit status | |
| configure:7145: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | /* end confdefs.h. */ | |
| | #include <pthread.h> | |
| | static void routine(void *a) { a = 0; } | |
| | static void *start_routine(void *a) { return a; } | |
| | int | |
| | main () | |
| | { | |
| | pthread_t th; pthread_attr_t attr; | |
| | pthread_create(&th, 0, start_routine, 0); | |
| | pthread_join(th, 0); | |
| | pthread_attr_init(&attr); | |
| | pthread_cleanup_push(routine, 0); | |
| | pthread_cleanup_pop(0) /* ; */ | |
| | ; | |
| | return 0; | |
| | } | |
| configure:7154: result: no | |
| configure:7057: checking whether pthreads work with -pthread | |
| configure:7145: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -pthread -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:7145: $? = 0 | |
| configure:7154: result: yes | |
| configure:7173: checking for joinable pthread attribute | |
| configure:7188: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -pthread -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:7188: $? = 0 | |
| configure:7194: result: PTHREAD_CREATE_JOINABLE | |
| configure:7204: checking if more special flags are required for pthreads | |
| configure:7219: result: no | |
| configure:7225: checking for PTHREAD_PRIO_INHERIT | |
| configure:7242: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -pthread -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c >&5 | |
| configure:7242: $? = 0 | |
| configure:7251: result: yes | |
| configure:7367: checking mpi.h usability | |
| configure:7367: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.c >&5 | |
| configure:7367: $? = 0 | |
| configure:7367: result: yes | |
| configure:7367: checking mpi.h presence | |
| configure:7367: /gsc/btl/linuxbrew/bin/gcc-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.c | |
| configure:7367: $? = 0 | |
| configure:7367: result: yes | |
| configure:7367: checking for mpi.h | |
| configure:7367: result: yes | |
| configure:7747: checking for MPI_Init in -lmpi | |
| configure:7772: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c -lmpi >&5 | |
| configure:7772: $? = 0 | |
| configure:7781: result: yes | |
| configure:7806: checking for sqrt in -lm | |
| configure:7831: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c -lm >&5 | |
| configure:7831: $? = 0 | |
| configure:7840: result: yes | |
| configure:7854: checking for pow | |
| configure:7854: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c -lm >&5 | |
| configure:7854: $? = 0 | |
| configure:7854: result: yes | |
| configure:7854: checking for sqrt | |
| configure:7854: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c -lm >&5 | |
| configure:7854: $? = 0 | |
| configure:7854: result: yes | |
| configure:7863: checking for ceilf | |
| configure:7863: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c -lm >&5 | |
| configure:7863: $? = 0 | |
| configure:7863: result: yes | |
| configure:7874: checking for dlsym in -ldl | |
| configure:7899: /gsc/btl/linuxbrew/bin/gcc-5 -o conftest -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.c -ldl -lm >&5 | |
| configure:7899: $? = 0 | |
| configure:7908: result: yes | |
| configure:7933: /gsc/btl/linuxbrew/bin/gcc-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.c >&5 | |
| configure:7933: $? = 0 | |
| configure:7956: checking how to run the C++ preprocessor | |
| configure:7983: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| configure:7983: $? = 0 | |
| configure:7997: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| conftest.cpp:64:28: fatal error: ac_nonexistent.h: No such file or directory | |
| compilation terminated. | |
| configure:7997: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | #define HAVE_PTHREAD_PRIO_INHERIT 1 | |
| | #define MPICH_SKIP_MPICXX 1 | |
| | #define OMPI_SKIP_MPICXX 1 | |
| | #define HAVE_MPI_H 1 | |
| | #define HAVE_LIBMPI 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_LIBDL 1 | |
| | #define HAVE_POPCNT 1 | |
| | /* end confdefs.h. */ | |
| | #include <ac_nonexistent.h> | |
| configure:8022: result: /gsc/btl/linuxbrew/bin/g++-5 -E | |
| configure:8042: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| configure:8042: $? = 0 | |
| configure:8056: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| conftest.cpp:64:28: fatal error: ac_nonexistent.h: No such file or directory | |
| compilation terminated. | |
| configure:8056: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | #define HAVE_PTHREAD_PRIO_INHERIT 1 | |
| | #define MPICH_SKIP_MPICXX 1 | |
| | #define OMPI_SKIP_MPICXX 1 | |
| | #define HAVE_MPI_H 1 | |
| | #define HAVE_LIBMPI 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_LIBDL 1 | |
| | #define HAVE_POPCNT 1 | |
| | /* end confdefs.h. */ | |
| | #include <ac_nonexistent.h> | |
| configure:8097: checking functional usability | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp >&5 | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking functional presence | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking for functional | |
| configure:8097: result: yes | |
| configure:8097: checking tr1/functional usability | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp >&5 | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking tr1/functional presence | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking for tr1/functional | |
| configure:8097: result: yes | |
| configure:8097: checking boost/functional/hash.hpp usability | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp >&5 | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking boost/functional/hash.hpp presence | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking for boost/functional/hash.hpp | |
| configure:8097: result: yes | |
| configure:8097: checking boost/property_map/property_map.hpp usability | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp >&5 | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking boost/property_map/property_map.hpp presence | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking for boost/property_map/property_map.hpp | |
| configure:8097: result: yes | |
| configure:8097: checking google/sparse_hash_map usability | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp >&5 | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking google/sparse_hash_map presence | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking for google/sparse_hash_map | |
| configure:8097: result: yes | |
| configure:8097: checking unordered_map usability | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp >&5 | |
| In file included from /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:35:0, | |
| from conftest.cpp:102: | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options. | |
| #error This file requires compiler and library support for the \ | |
| ^ | |
| configure:8097: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | #define HAVE_PTHREAD_PRIO_INHERIT 1 | |
| | #define MPICH_SKIP_MPICXX 1 | |
| | #define OMPI_SKIP_MPICXX 1 | |
| | #define HAVE_MPI_H 1 | |
| | #define HAVE_LIBMPI 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_LIBDL 1 | |
| | #define HAVE_POPCNT 1 | |
| | #define HAVE_FUNCTIONAL 1 | |
| | #define HAVE_TR1_FUNCTIONAL 1 | |
| | #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1 | |
| | #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1 | |
| | #define HAVE_GOOGLE_SPARSE_HASH_MAP 1 | |
| | /* end confdefs.h. */ | |
| | #include <stdio.h> | |
| | #ifdef HAVE_SYS_TYPES_H | |
| | # include <sys/types.h> | |
| | #endif | |
| | #ifdef HAVE_SYS_STAT_H | |
| | # include <sys/stat.h> | |
| | #endif | |
| | #ifdef STDC_HEADERS | |
| | # include <stdlib.h> | |
| | # include <stddef.h> | |
| | #else | |
| | # ifdef HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | # endif | |
| | #endif | |
| | #ifdef HAVE_STRING_H | |
| | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | |
| | # include <memory.h> | |
| | # endif | |
| | # include <string.h> | |
| | #endif | |
| | #ifdef HAVE_STRINGS_H | |
| | # include <strings.h> | |
| | #endif | |
| | #ifdef HAVE_INTTYPES_H | |
| | # include <inttypes.h> | |
| | #endif | |
| | #ifdef HAVE_STDINT_H | |
| | # include <stdint.h> | |
| | #endif | |
| | #ifdef HAVE_UNISTD_H | |
| | # include <unistd.h> | |
| | #endif | |
| | #include <unordered_map> | |
| configure:8097: result: no | |
| configure:8097: checking unordered_map presence | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| In file included from /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_map:35:0, | |
| from conftest.cpp:69: | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options. | |
| #error This file requires compiler and library support for the \ | |
| ^ | |
| configure:8097: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | #define HAVE_PTHREAD_PRIO_INHERIT 1 | |
| | #define MPICH_SKIP_MPICXX 1 | |
| | #define OMPI_SKIP_MPICXX 1 | |
| | #define HAVE_MPI_H 1 | |
| | #define HAVE_LIBMPI 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_LIBDL 1 | |
| | #define HAVE_POPCNT 1 | |
| | #define HAVE_FUNCTIONAL 1 | |
| | #define HAVE_TR1_FUNCTIONAL 1 | |
| | #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1 | |
| | #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1 | |
| | #define HAVE_GOOGLE_SPARSE_HASH_MAP 1 | |
| | /* end confdefs.h. */ | |
| | #include <unordered_map> | |
| configure:8097: result: no | |
| configure:8097: checking for unordered_map | |
| configure:8097: result: no | |
| configure:8097: checking tr1/unordered_map usability | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp >&5 | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking tr1/unordered_map presence | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking for tr1/unordered_map | |
| configure:8097: result: yes | |
| configure:8097: checking unordered_set usability | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp >&5 | |
| In file included from /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_set:35:0, | |
| from conftest.cpp:103: | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options. | |
| #error This file requires compiler and library support for the \ | |
| ^ | |
| configure:8097: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | #define HAVE_PTHREAD_PRIO_INHERIT 1 | |
| | #define MPICH_SKIP_MPICXX 1 | |
| | #define OMPI_SKIP_MPICXX 1 | |
| | #define HAVE_MPI_H 1 | |
| | #define HAVE_LIBMPI 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_LIBDL 1 | |
| | #define HAVE_POPCNT 1 | |
| | #define HAVE_FUNCTIONAL 1 | |
| | #define HAVE_TR1_FUNCTIONAL 1 | |
| | #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1 | |
| | #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1 | |
| | #define HAVE_GOOGLE_SPARSE_HASH_MAP 1 | |
| | #define HAVE_TR1_UNORDERED_MAP 1 | |
| | /* end confdefs.h. */ | |
| | #include <stdio.h> | |
| | #ifdef HAVE_SYS_TYPES_H | |
| | # include <sys/types.h> | |
| | #endif | |
| | #ifdef HAVE_SYS_STAT_H | |
| | # include <sys/stat.h> | |
| | #endif | |
| | #ifdef STDC_HEADERS | |
| | # include <stdlib.h> | |
| | # include <stddef.h> | |
| | #else | |
| | # ifdef HAVE_STDLIB_H | |
| | # include <stdlib.h> | |
| | # endif | |
| | #endif | |
| | #ifdef HAVE_STRING_H | |
| | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | |
| | # include <memory.h> | |
| | # endif | |
| | # include <string.h> | |
| | #endif | |
| | #ifdef HAVE_STRINGS_H | |
| | # include <strings.h> | |
| | #endif | |
| | #ifdef HAVE_INTTYPES_H | |
| | # include <inttypes.h> | |
| | #endif | |
| | #ifdef HAVE_STDINT_H | |
| | # include <stdint.h> | |
| | #endif | |
| | #ifdef HAVE_UNISTD_H | |
| | # include <unistd.h> | |
| | #endif | |
| | #include <unordered_set> | |
| configure:8097: result: no | |
| configure:8097: checking unordered_set presence | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| In file included from /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/unordered_set:35:0, | |
| from conftest.cpp:70: | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/include/c++/5.3.0/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options. | |
| #error This file requires compiler and library support for the \ | |
| ^ | |
| configure:8097: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | #define HAVE_PTHREAD_PRIO_INHERIT 1 | |
| | #define MPICH_SKIP_MPICXX 1 | |
| | #define OMPI_SKIP_MPICXX 1 | |
| | #define HAVE_MPI_H 1 | |
| | #define HAVE_LIBMPI 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_LIBDL 1 | |
| | #define HAVE_POPCNT 1 | |
| | #define HAVE_FUNCTIONAL 1 | |
| | #define HAVE_TR1_FUNCTIONAL 1 | |
| | #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1 | |
| | #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1 | |
| | #define HAVE_GOOGLE_SPARSE_HASH_MAP 1 | |
| | #define HAVE_TR1_UNORDERED_MAP 1 | |
| | /* end confdefs.h. */ | |
| | #include <unordered_set> | |
| configure:8097: result: no | |
| configure:8097: checking for unordered_set | |
| configure:8097: result: no | |
| configure:8097: checking tr1/unordered_set usability | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp >&5 | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking tr1/unordered_set presence | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking for tr1/unordered_set | |
| configure:8097: result: yes | |
| configure:8097: checking boost/unordered_set.hpp usability | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp >&5 | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking boost/unordered_set.hpp presence | |
| configure:8097: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| configure:8097: $? = 0 | |
| configure:8097: result: yes | |
| configure:8097: checking for boost/unordered_set.hpp | |
| configure:8097: result: yes | |
| configure:8125: checking sqlite3.h usability | |
| configure:8125: /gsc/btl/linuxbrew/bin/g++-5 -c -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp >&5 | |
| configure:8125: $? = 0 | |
| configure:8125: result: yes | |
| configure:8125: checking sqlite3.h presence | |
| configure:8125: /gsc/btl/linuxbrew/bin/g++-5 -E -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 conftest.cpp | |
| configure:8125: $? = 0 | |
| configure:8125: result: yes | |
| configure:8125: checking for sqlite3.h | |
| configure:8125: result: yes | |
| configure:8135: checking for main in -lsqlite3 | |
| configure:8154: /gsc/btl/linuxbrew/bin/g++-5 -o conftest -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.cpp -lsqlite3 -ldl -lm >&5 | |
| configure:8154: $? = 0 | |
| configure:8163: result: yes | |
| configure:8201: checking for /gsc/btl/linuxbrew/bin/g++-5 option to support OpenMP | |
| configure:8216: /gsc/btl/linuxbrew/bin/g++-5 -o conftest -Os -w -pipe -march=native -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.cpp -ldl -lm >&5 | |
| conftest.cpp:77:2: error: 'choke' does not name a type | |
| choke me | |
| ^ | |
| In file included from conftest.cpp:79:0: | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:39:3: error: 'omp_lock_t' does not name a type | |
| } omp_lock_t; | |
| ^ | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:86:28: error: variable or field 'omp_init_lock' declared void | |
| extern void omp_init_lock (omp_lock_t *) __GOMP_NOTHROW; | |
| ^ | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:86:28: error: 'omp_lock_t' was not declared in this scope | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:86:40: error: expected primary-expression before ')' token | |
| extern void omp_init_lock (omp_lock_t *) __GOMP_NOTHROW; | |
| ^ | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:87:31: error: variable or field 'omp_destroy_lock' declared void | |
| extern void omp_destroy_lock (omp_lock_t *) __GOMP_NOTHROW; | |
| ^ | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:87:31: error: 'omp_lock_t' was not declared in this scope | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:87:43: error: expected primary-expression before ')' token | |
| extern void omp_destroy_lock (omp_lock_t *) __GOMP_NOTHROW; | |
| ^ | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:88:27: error: variable or field 'omp_set_lock' declared void | |
| extern void omp_set_lock (omp_lock_t *) __GOMP_NOTHROW; | |
| ^ | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:88:27: error: 'omp_lock_t' was not declared in this scope | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:88:39: error: expected primary-expression before ')' token | |
| extern void omp_set_lock (omp_lock_t *) __GOMP_NOTHROW; | |
| ^ | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:89:29: error: variable or field 'omp_unset_lock' declared void | |
| extern void omp_unset_lock (omp_lock_t *) __GOMP_NOTHROW; | |
| ^ | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:89:29: error: 'omp_lock_t' was not declared in this scope | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:89:41: error: expected primary-expression before ')' token | |
| extern void omp_unset_lock (omp_lock_t *) __GOMP_NOTHROW; | |
| ^ | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:90:27: error: 'omp_lock_t' was not declared in this scope | |
| extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW; | |
| ^ | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:90:39: error: expected primary-expression before ')' token | |
| extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW; | |
| ^ | |
| /gsc/btl/linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include/omp.h:90:41: error: expected ',' or ';' before 'throw' | |
| extern int omp_test_lock (omp_lock_t *) __GOMP_NOTHROW; | |
| ^ | |
| configure:8216: $? = 1 | |
| configure: failed program was: | |
| | /* confdefs.h */ | |
| | #define PACKAGE_NAME "ABySS" | |
| | #define PACKAGE_TARNAME "abyss" | |
| | #define PACKAGE_VERSION "2.0.1" | |
| | #define PACKAGE_STRING "ABySS 2.0.1" | |
| | #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| | #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| | #define PACKAGE "abyss" | |
| | #define VERSION "2.0.1" | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_SYS_TYPES_H 1 | |
| | #define HAVE_SYS_STAT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_STRING_H 1 | |
| | #define HAVE_MEMORY_H 1 | |
| | #define HAVE_STRINGS_H 1 | |
| | #define HAVE_INTTYPES_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_UNISTD_H 1 | |
| | #define HAVE_DLFCN_H 1 | |
| | #define HAVE_FCNTL_H 1 | |
| | #define HAVE_FLOAT_H 1 | |
| | #define HAVE_LIMITS_H 1 | |
| | #define HAVE_STDDEF_H 1 | |
| | #define HAVE_STDINT_H 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_SYS_PARAM_H 1 | |
| | #define HAVE__BOOL 1 | |
| | #define HAVE_STDBOOL_H 1 | |
| | #define STDC_HEADERS 1 | |
| | #define HAVE_PTRDIFF_T 1 | |
| | #define HAVE_STD_TR1_HASH 1 | |
| | #define HAVE_DUP2 1 | |
| | #define HAVE_GETHOSTNAME 1 | |
| | #define HAVE_GETOPT_LONG 1 | |
| | #define HAVE_GETPAGESIZE 1 | |
| | #define HAVE_MEMSET 1 | |
| | #define HAVE_STRDUP 1 | |
| | #define HAVE_STRERROR 1 | |
| | #define HAVE_STRTOUL 1 | |
| | #define HAVE_FORK 1 | |
| | #define HAVE_VFORK 1 | |
| | #define HAVE_WORKING_VFORK 1 | |
| | #define HAVE_WORKING_FORK 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_MALLOC 1 | |
| | #define HAVE_STDLIB_H 1 | |
| | #define HAVE_REALLOC 1 | |
| | #define HAVE_VPRINTF 1 | |
| | #define FMBITS 64 | |
| | #define MAX_KMER 160 | |
| | #define MAX_HASHES 32 | |
| | #define HAVE_PTHREAD_PRIO_INHERIT 1 | |
| | #define MPICH_SKIP_MPICXX 1 | |
| | #define OMPI_SKIP_MPICXX 1 | |
| | #define HAVE_MPI_H 1 | |
| | #define HAVE_LIBMPI 1 | |
| | #define HAVE_LIBM 1 | |
| | #define HAVE_POW 1 | |
| | #define HAVE_SQRT 1 | |
| | #define HAVE_LIBDL 1 | |
| | #define HAVE_POPCNT 1 | |
| | #define HAVE_FUNCTIONAL 1 | |
| | #define HAVE_TR1_FUNCTIONAL 1 | |
| | #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1 | |
| | #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1 | |
| | #define HAVE_GOOGLE_SPARSE_HASH_MAP 1 | |
| | #define HAVE_TR1_UNORDERED_MAP 1 | |
| | #define HAVE_TR1_UNORDERED_SET 1 | |
| | #define HAVE_BOOST_UNORDERED_SET_HPP 1 | |
| | #define HAVE_SQLITE3_H 1 | |
| | #define HAVE_LIBSQLITE3 1 | |
| | #define _SQL 1 | |
| | /* end confdefs.h. */ | |
| | | |
| | #ifndef _OPENMP | |
| | choke me | |
| | #endif | |
| | #include <omp.h> | |
| | int main () { return omp_get_num_threads (); } | |
| | | |
| configure:8234: /gsc/btl/linuxbrew/bin/g++-5 -o conftest -Os -w -pipe -march=native -fopenmp -I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0 -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib conftest.cpp -ldl -lm >&5 | |
| configure:8234: $? = 0 | |
| configure:8248: result: -fopenmp | |
| configure:8420: checking that generated files are newer than configure | |
| configure:8426: result: done | |
| configure:8478: creating ./config.status | |
| ## ---------------------- ## | |
| ## Running config.status. ## | |
| ## ---------------------- ## | |
| This file was extended by ABySS config.status 2.0.1, which was | |
| generated by GNU Autoconf 2.69. Invocation command line was | |
| CONFIG_FILES = | |
| CONFIG_HEADERS = | |
| CONFIG_LINKS = | |
| CONFIG_COMMANDS = | |
| $ ./config.status | |
| on gphost02 | |
| config.status:987: creating Makefile | |
| config.status:987: creating ABYSS/Makefile | |
| config.status:987: creating Align/Makefile | |
| config.status:987: creating Assembly/Makefile | |
| config.status:987: creating Common/Makefile | |
| config.status:987: creating DataLayer/Makefile | |
| config.status:987: creating FMIndex/Makefile | |
| config.status:987: creating Graph/Makefile | |
| config.status:987: creating Parallel/Makefile | |
| config.status:987: creating bin/Makefile | |
| config.status:987: creating doc/Makefile | |
| config.status:987: creating dialign/Makefile | |
| config.status:987: creating kmerprint/Makefile | |
| config.status:987: creating AdjList/Makefile | |
| config.status:987: creating Konnector/Makefile | |
| config.status:987: creating DAssembler/Makefile | |
| config.status:987: creating DistanceEst/Makefile | |
| config.status:987: creating Layout/Makefile | |
| config.status:987: creating Map/Makefile | |
| config.status:987: creating Misc/Makefile | |
| config.status:987: creating Overlap/Makefile | |
| config.status:987: creating PopBubbles/Makefile | |
| config.status:987: creating Scaffold/Makefile | |
| config.status:987: creating SimpleGraph/Makefile | |
| config.status:987: creating MergePaths/Makefile | |
| config.status:987: creating KAligner/Makefile | |
| config.status:987: creating PairedDBG/Makefile | |
| config.status:987: creating ParseAligns/Makefile | |
| config.status:987: creating PathOverlap/Makefile | |
| config.status:987: creating Consensus/Makefile | |
| config.status:987: creating FilterGraph/Makefile | |
| config.status:987: creating GapFiller/Makefile | |
| config.status:987: creating Sealer/Makefile | |
| config.status:987: creating lib/gtest-1.7.0/Makefile | |
| config.status:987: creating Unittest/Makefile | |
| config.status:987: creating LogKmerCount/Makefile | |
| config.status:987: creating Bloom/Makefile | |
| config.status:987: creating BloomDBG/Makefile | |
| config.status:987: creating DataBase/Makefile | |
| config.status:987: creating lib/bloomfilter/Makefile | |
| config.status:987: creating lib/rolling-hash/Makefile | |
| config.status:987: creating config.h | |
| config.status:1216: executing depfiles commands | |
| ## ---------------- ## | |
| ## Cache variables. ## | |
| ## ---------------- ## | |
| ac_cv_build=x86_64-unknown-linux-gnu | |
| ac_cv_c_bigendian=no | |
| ac_cv_c_compiler_gnu=yes | |
| ac_cv_c_const=yes | |
| ac_cv_c_inline=inline | |
| ac_cv_c_int64_t=yes | |
| ac_cv_c_uint16_t=yes | |
| ac_cv_c_uint32_t=yes | |
| ac_cv_c_uint64_t=yes | |
| ac_cv_c_uint8_t=yes | |
| ac_cv_cxx_compiler_gnu=yes | |
| ac_cv_env_CCC_set= | |
| ac_cv_env_CCC_value= | |
| ac_cv_env_CC_set=set | |
| ac_cv_env_CC_value=/gsc/btl/linuxbrew/bin/gcc-5 | |
| ac_cv_env_CFLAGS_set=set | |
| ac_cv_env_CFLAGS_value='-Os -w -pipe -march=native' | |
| ac_cv_env_CPPFLAGS_set=set | |
| ac_cv_env_CPPFLAGS_value=-isystem/gsc/btl/linuxbrew/include | |
| ac_cv_env_CPP_set= | |
| ac_cv_env_CPP_value= | |
| ac_cv_env_CXXCPP_set= | |
| ac_cv_env_CXXCPP_value= | |
| ac_cv_env_CXXFLAGS_set=set | |
| ac_cv_env_CXXFLAGS_value='-Os -w -pipe -march=native' | |
| ac_cv_env_CXX_set=set | |
| ac_cv_env_CXX_value=/gsc/btl/linuxbrew/bin/g++-5 | |
| ac_cv_env_LDFLAGS_set=set | |
| ac_cv_env_LDFLAGS_value='-L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib' | |
| ac_cv_env_LIBS_set= | |
| ac_cv_env_LIBS_value= | |
| ac_cv_env_build_alias_set= | |
| ac_cv_env_build_alias_value= | |
| ac_cv_env_host_alias_set= | |
| ac_cv_env_host_alias_value= | |
| ac_cv_env_target_alias_set= | |
| ac_cv_env_target_alias_value= | |
| ac_cv_func__doprnt=no | |
| ac_cv_func_ceilf=yes | |
| ac_cv_func_dup2=yes | |
| ac_cv_func_fork=yes | |
| ac_cv_func_fork_works=yes | |
| ac_cv_func_gethostname=yes | |
| ac_cv_func_getopt_long=yes | |
| ac_cv_func_getpagesize=yes | |
| ac_cv_func_malloc_0_nonnull=yes | |
| ac_cv_func_memcmp_working=yes | |
| ac_cv_func_memset=yes | |
| ac_cv_func_pow=yes | |
| ac_cv_func_realloc_0_nonnull=yes | |
| ac_cv_func_setvbuf_reversed=no | |
| ac_cv_func_sqrt=yes | |
| ac_cv_func_strdup=yes | |
| ac_cv_func_strerror=yes | |
| ac_cv_func_strtoul=yes | |
| ac_cv_func_vfork=yes | |
| ac_cv_func_vfork_works=yes | |
| ac_cv_func_vprintf=yes | |
| ac_cv_have_decl_HOST_NAME_MAX=yes | |
| ac_cv_header_boost_functional_hash_hpp=yes | |
| ac_cv_header_boost_property_map_property_map_hpp=yes | |
| ac_cv_header_boost_unordered_set_hpp=yes | |
| ac_cv_header_dlfcn_h=yes | |
| ac_cv_header_fcntl_h=yes | |
| ac_cv_header_float_h=yes | |
| ac_cv_header_functional=yes | |
| ac_cv_header_google_sparse_hash_map=yes | |
| ac_cv_header_inttypes_h=yes | |
| ac_cv_header_limits_h=yes | |
| ac_cv_header_memory_h=yes | |
| ac_cv_header_mpi_h=yes | |
| ac_cv_header_sqlite3_h=yes | |
| ac_cv_header_stdbool_h=yes | |
| ac_cv_header_stdc=yes | |
| ac_cv_header_stddef_h=yes | |
| ac_cv_header_stdint_h=yes | |
| ac_cv_header_stdlib_h=yes | |
| ac_cv_header_string_h=yes | |
| ac_cv_header_strings_h=yes | |
| ac_cv_header_sys_param_h=yes | |
| ac_cv_header_sys_stat_h=yes | |
| ac_cv_header_sys_types_h=yes | |
| ac_cv_header_tr1_functional=yes | |
| ac_cv_header_tr1_unordered_map=yes | |
| ac_cv_header_tr1_unordered_set=yes | |
| ac_cv_header_unistd_h=yes | |
| ac_cv_header_unordered_map=no | |
| ac_cv_header_unordered_set=no | |
| ac_cv_header_vfork_h=no | |
| ac_cv_host=x86_64-unknown-linux-gnu | |
| ac_cv_lib_dl_dlsym=yes | |
| ac_cv_lib_m_sqrt=yes | |
| ac_cv_lib_mpi_MPI_Init=yes | |
| ac_cv_lib_sqlite3_main=yes | |
| ac_cv_objext=o | |
| ac_cv_path_EGREP='/gsc/btl/linuxbrew/bin/grep -E' | |
| ac_cv_path_GREP=/gsc/btl/linuxbrew/bin/grep | |
| ac_cv_path_install='/gsc/btl/linuxbrew/bin/ginstall -c' | |
| ac_cv_path_mkdir=/gsc/btl/linuxbrew/bin/mkdir | |
| ac_cv_prog_AWK=gawk | |
| ac_cv_prog_CPP='/gsc/btl/linuxbrew/bin/gcc-5 -E' | |
| ac_cv_prog_CXXCPP='/gsc/btl/linuxbrew/bin/g++-5 -E' | |
| ac_cv_prog_PANDOC=yes | |
| ac_cv_prog_ac_ct_CC=/gsc/btl/linuxbrew/bin/gcc-5 | |
| ac_cv_prog_ac_ct_GHC=ghc | |
| ac_cv_prog_ac_ct_GHC_PKG=ghc-pkg | |
| ac_cv_prog_ac_ct_RANLIB=ranlib | |
| ac_cv_prog_cc_c89= | |
| ac_cv_prog_cc_g=yes | |
| ac_cv_prog_cxx_g=yes | |
| ac_cv_prog_cxx_openmp=-fopenmp | |
| ac_cv_prog_make_make_set=yes | |
| ac_cv_type__Bool=yes | |
| ac_cv_type_mode_t=yes | |
| ac_cv_type_pid_t=yes | |
| ac_cv_type_ptrdiff_t=yes | |
| ac_cv_type_size_t=yes | |
| ac_cv_type_ssize_t=yes | |
| ac_cv_type_std__hash_int_=no | |
| ac_cv_type_std__tr1__hash_int_=yes | |
| am_cv_CC_dependencies_compiler_type=none | |
| am_cv_CXX_dependencies_compiler_type=none | |
| am_cv_make_support_nested_variables=yes | |
| ax_cv_PTHREAD_PRIO_INHERIT=yes | |
| ## ----------------- ## | |
| ## Output variables. ## | |
| ## ----------------- ## | |
| ACLOCAL='${SHELL} /var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/missing aclocal-1.13' | |
| AMDEPBACKSLASH='' | |
| AMDEP_FALSE='' | |
| AMDEP_TRUE='#' | |
| AMTAR='$${TAR-tar}' | |
| AM_BACKSLASH='\' | |
| AM_CXXFLAGS='-Wall -Wextra' | |
| AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)' | |
| AM_DEFAULT_VERBOSITY='1' | |
| AM_V='$(V)' | |
| AUTOCONF='${SHELL} /var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/missing autoconf' | |
| AUTOHEADER='${SHELL} /var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/missing autoheader' | |
| AUTOMAKE='${SHELL} /var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/missing automake-1.13' | |
| AWK='gawk' | |
| CC='/gsc/btl/linuxbrew/bin/gcc-5' | |
| CCDEPMODE='depmode=none' | |
| CFLAGS='-Os -w -pipe -march=native' | |
| CPP='/gsc/btl/linuxbrew/bin/gcc-5 -E' | |
| CPPFLAGS='-I/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1 -isystem/gsc/btl/linuxbrew/include -isystem/var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/boost_1_56_0' | |
| CXX='/gsc/btl/linuxbrew/bin/g++-5' | |
| CXXCPP='/gsc/btl/linuxbrew/bin/g++-5 -E' | |
| CXXDEPMODE='depmode=none' | |
| CXXFLAGS='-Os -w -pipe -march=native' | |
| CYGPATH_W='echo' | |
| DEFS='-DHAVE_CONFIG_H' | |
| DEPDIR='.deps' | |
| ECHO_C='' | |
| ECHO_N='-n' | |
| ECHO_T='' | |
| EGREP='/gsc/btl/linuxbrew/bin/grep -E' | |
| EXEEXT='' | |
| GHC='ghc' | |
| GHC_PKG='ghc-pkg' | |
| GREP='/gsc/btl/linuxbrew/bin/grep' | |
| HAVE_GHC_MMAP_FALSE='' | |
| HAVE_GHC_MMAP_TRUE='#' | |
| HAVE_LIBMPI_FALSE='#' | |
| HAVE_LIBMPI_TRUE='' | |
| HAVE_PANDOC_FALSE='#' | |
| HAVE_PANDOC_TRUE='' | |
| HAVE_PTHREAD_FALSE='#' | |
| HAVE_PTHREAD_TRUE='' | |
| HAVE_SQLITE3_FALSE='#' | |
| HAVE_SQLITE3_TRUE='' | |
| INSTALL_DATA='${INSTALL} -m 644' | |
| INSTALL_PROGRAM='${INSTALL}' | |
| INSTALL_SCRIPT='${INSTALL}' | |
| INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' | |
| LDFLAGS=' -L/gsc/btl/linuxbrew/lib -Wl,--dynamic-linker=/gsc/btl/linuxbrew/lib/ld.so -Wl,-rpath,/gsc/btl/linuxbrew/lib' | |
| LIBOBJS='' | |
| LIBS='-ldl -lm ' | |
| LTLIBOBJS='' | |
| MAKEINFO='${SHELL} /var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/missing makeinfo' | |
| MKDIR_P='/gsc/btl/linuxbrew/bin/mkdir -p' | |
| MPI_LIBS='-lmpi ' | |
| OBJEXT='o' | |
| OPENMP_CXXFLAGS='-fopenmp' | |
| PACKAGE='abyss' | |
| PACKAGE_BUGREPORT='abyss-users@bcgsc.ca' | |
| PACKAGE_NAME='ABySS' | |
| PACKAGE_STRING='ABySS 2.0.1' | |
| PACKAGE_TARNAME='abyss' | |
| PACKAGE_URL='http://www.bcgsc.ca/platform/bioinfo/software/abyss' | |
| PACKAGE_VERSION='2.0.1' | |
| PAIRED_DBG_FALSE='#' | |
| PAIRED_DBG_TRUE='' | |
| PANDOC='yes' | |
| PATH_SEPARATOR=':' | |
| PTHREAD_CC='/gsc/btl/linuxbrew/bin/gcc-5' | |
| PTHREAD_CFLAGS='-pthread' | |
| PTHREAD_LIBS='' | |
| RANLIB='ranlib' | |
| SET_MAKE='' | |
| SHELL='/bin/sh' | |
| SQLITE_LIBS='-lsqlite3 -ldl -lm ' | |
| STRIP='' | |
| VERSION='2.0.1' | |
| ac_ct_CC='/gsc/btl/linuxbrew/bin/gcc-5' | |
| ac_ct_CXX='' | |
| am__EXEEXT_FALSE='' | |
| am__EXEEXT_TRUE='#' | |
| am__fastdepCC_FALSE='' | |
| am__fastdepCC_TRUE='#' | |
| am__fastdepCXX_FALSE='' | |
| am__fastdepCXX_TRUE='#' | |
| am__include='include' | |
| am__isrc='' | |
| am__leading_dot='.' | |
| am__nodep='' | |
| am__quote='' | |
| am__tar='$${TAR-tar} chof - "$$tardir"' | |
| am__untar='$${TAR-tar} xf -' | |
| ax_pthread_config='' | |
| bindir='${exec_prefix}/bin' | |
| build='x86_64-unknown-linux-gnu' | |
| build_alias='' | |
| build_cpu='x86_64' | |
| build_os='linux-gnu' | |
| build_vendor='unknown' | |
| datadir='${datarootdir}' | |
| datarootdir='${prefix}/share' | |
| docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' | |
| dvidir='${docdir}' | |
| exec_prefix='${prefix}' | |
| host='x86_64-unknown-linux-gnu' | |
| host_alias='' | |
| host_cpu='x86_64' | |
| host_os='linux-gnu' | |
| host_vendor='unknown' | |
| htmldir='${docdir}' | |
| includedir='${prefix}/include' | |
| infodir='${datarootdir}/info' | |
| install_sh='${SHELL} /var/tmp/sjackman/abyss-20160925-117577-1yv2ux6/abyss-2.0.1/install-sh' | |
| libdir='${exec_prefix}/lib' | |
| libexecdir='${exec_prefix}/libexec' | |
| localedir='${datarootdir}/locale' | |
| localstatedir='${prefix}/var' | |
| mandir='${datarootdir}/man' | |
| mkdir_p='$(MKDIR_P)' | |
| oldincludedir='/usr/include' | |
| pdfdir='${docdir}' | |
| prefix='/gsc/btl/linuxbrew/Cellar/abyss/2.0.1' | |
| program_transform_name='s,x,x,' | |
| psdir='${docdir}' | |
| sbindir='${exec_prefix}/sbin' | |
| sharedstatedir='${prefix}/com' | |
| sysconfdir='${prefix}/etc' | |
| target_alias='' | |
| ## ----------- ## | |
| ## confdefs.h. ## | |
| ## ----------- ## | |
| /* confdefs.h */ | |
| #define PACKAGE_NAME "ABySS" | |
| #define PACKAGE_TARNAME "abyss" | |
| #define PACKAGE_VERSION "2.0.1" | |
| #define PACKAGE_STRING "ABySS 2.0.1" | |
| #define PACKAGE_BUGREPORT "abyss-users@bcgsc.ca" | |
| #define PACKAGE_URL "http://www.bcgsc.ca/platform/bioinfo/software/abyss" | |
| #define PACKAGE "abyss" | |
| #define VERSION "2.0.1" | |
| #define STDC_HEADERS 1 | |
| #define HAVE_SYS_TYPES_H 1 | |
| #define HAVE_SYS_STAT_H 1 | |
| #define HAVE_STDLIB_H 1 | |
| #define HAVE_STRING_H 1 | |
| #define HAVE_MEMORY_H 1 | |
| #define HAVE_STRINGS_H 1 | |
| #define HAVE_INTTYPES_H 1 | |
| #define HAVE_STDINT_H 1 | |
| #define HAVE_UNISTD_H 1 | |
| #define HAVE_DLFCN_H 1 | |
| #define HAVE_FCNTL_H 1 | |
| #define HAVE_FLOAT_H 1 | |
| #define HAVE_LIMITS_H 1 | |
| #define HAVE_STDDEF_H 1 | |
| #define HAVE_STDINT_H 1 | |
| #define HAVE_STDLIB_H 1 | |
| #define HAVE_SYS_PARAM_H 1 | |
| #define HAVE__BOOL 1 | |
| #define HAVE_STDBOOL_H 1 | |
| #define STDC_HEADERS 1 | |
| #define HAVE_PTRDIFF_T 1 | |
| #define HAVE_STD_TR1_HASH 1 | |
| #define HAVE_DUP2 1 | |
| #define HAVE_GETHOSTNAME 1 | |
| #define HAVE_GETOPT_LONG 1 | |
| #define HAVE_GETPAGESIZE 1 | |
| #define HAVE_MEMSET 1 | |
| #define HAVE_STRDUP 1 | |
| #define HAVE_STRERROR 1 | |
| #define HAVE_STRTOUL 1 | |
| #define HAVE_FORK 1 | |
| #define HAVE_VFORK 1 | |
| #define HAVE_WORKING_VFORK 1 | |
| #define HAVE_WORKING_FORK 1 | |
| #define HAVE_STDLIB_H 1 | |
| #define HAVE_MALLOC 1 | |
| #define HAVE_STDLIB_H 1 | |
| #define HAVE_REALLOC 1 | |
| #define HAVE_VPRINTF 1 | |
| #define FMBITS 64 | |
| #define MAX_KMER 160 | |
| #define MAX_HASHES 32 | |
| #define HAVE_PTHREAD_PRIO_INHERIT 1 | |
| #define MPICH_SKIP_MPICXX 1 | |
| #define OMPI_SKIP_MPICXX 1 | |
| #define HAVE_MPI_H 1 | |
| #define HAVE_LIBMPI 1 | |
| #define HAVE_LIBM 1 | |
| #define HAVE_POW 1 | |
| #define HAVE_SQRT 1 | |
| #define HAVE_LIBDL 1 | |
| #define HAVE_POPCNT 1 | |
| #define HAVE_FUNCTIONAL 1 | |
| #define HAVE_TR1_FUNCTIONAL 1 | |
| #define HAVE_BOOST_FUNCTIONAL_HASH_HPP 1 | |
| #define HAVE_BOOST_PROPERTY_MAP_PROPERTY_MAP_HPP 1 | |
| #define HAVE_GOOGLE_SPARSE_HASH_MAP 1 | |
| #define HAVE_TR1_UNORDERED_MAP 1 | |
| #define HAVE_TR1_UNORDERED_SET 1 | |
| #define HAVE_BOOST_UNORDERED_SET_HPP 1 | |
| #define HAVE_SQLITE3_H 1 | |
| #define HAVE_LIBSQLITE3 1 | |
| #define _SQL 1 | |
| configure: exit 0 |
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