* Package: sci-biology/abyss-1.2.3 * Repository: gentoo * Maintainer: weaver@gentoo.org sci-biology@gentoo.org * USE: elibc_glibc kernel_linux mpi test userland_GNU x86 * FEATURES: sandbox test userpriv usersandbox >>> Unpacking source... >>> Unpacking abyss-1.2.3.tar.gz to /var/tmp/portage/sci-biology/abyss-1.2.3/work >>> Source unpacked in /var/tmp/portage/sci-biology/abyss-1.2.3/work >>> Preparing source in /var/tmp/portage/sci-biology/abyss-1.2.3/work/abyss-1.2.3 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/abyss-1.2.3/work/abyss-1.2.3 ... ./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib configure: loading site script /usr/share/config.site configure: loading site script /usr/share/crossdev/include/site/linux checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gawk... (cached) gawk checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc 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 i686-pc-linux-gnu-gcc accepts -g... yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-gcc... gcc3 checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether i686-pc-linux-gnu-g++ accepts -g... yes checking dependency style of i686-pc-linux-gnu-g++... gcc3 checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib checking for grep that handles long lines and -e... /bin/grep checking for egrep... /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 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 dup2... yes checking for gethostname... yes checking for getopt_long... 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 working memcmp... yes checking for vprintf... yes checking for _doprnt... no checking whether HOST_NAME_MAX is declared... 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... i686-pc-linux-gnu-g++ -E 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 ext/hash_map usability... yes checking ext/hash_map presence... yes checking for ext/hash_map... yes checking for i686-pc-linux-gnu-g++ option to support OpenMP... -fopenmp 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 Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating DistanceEst/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating config.h config.status: executing depfiles commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/abyss-1.2.3/work/abyss-1.2.3 ... make -j14 make all-recursive make[1]: Entering directory `/var/tmp/portage/sci-biology/abyss-1.2.3/work/abyss-1.2.3' Making all in Align make[2]: Entering directory `/var/tmp/portage/sci-biology/abyss-1.2.3/work/abyss-1.2.3/Align' i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -Wall -Wextra -Werror -O2 -pipe -MT libalign_a-Aligner.o -MD -MP -MF .deps/libalign_a-Aligner.Tpo -c -o libalign_a-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp Aligner.cpp: In member function ‘Aligner<SeqPosHashMap>::AlignmentSet Aligner<SeqPosHashMap>::getAlignmentsInternal(const Sequence&, bool) [with SeqPosHashMap = std::tr1::unordered_multimap<Kmer, Position, hashKmer>, Aligner<SeqPosHashMap>::AlignmentSet = std::map<unsigned int, std::vector<Alignment> >, Sequence = std::basic_string<char>]’: Aligner.cpp:78:2: instantiated from ‘void Aligner<SeqPosHashMap>::alignRead(const string&, const Sequence&, oiterator) [with oiterator = affix_ostream_iterator<Alignment>, SeqPosHashMap = std::tr1::unordered_multimap<Kmer, Position, hashKmer>, std::string = std::basic_string<char>, Sequence = std::basic_string<char>]’ Aligner.cpp:182:41: instantiated from here Aligner.cpp:94:7: error: variable ‘discarded’ set but not used [-Werror=unused-but-set-variable] Aligner.cpp: In member function ‘Aligner<SeqPosHashMap>::AlignmentSet Aligner<SeqPosHashMap>::getAlignmentsInternal(const Sequence&, bool) [with SeqPosHashMap = google::sparse_hash_map<Kmer, Position, hashKmer>, Aligner<SeqPosHashMap>::AlignmentSet = std::map<unsigned int, std::vector<Alignment> >, Sequence = std::basic_string<char>]’: Aligner.cpp:78:2: instantiated from ‘void Aligner<SeqPosHashMap>::alignRead(const string&, const Sequence&, oiterator) [with oiterator = affix_ostream_iterator<Alignment>, SeqPosHashMap = google::sparse_hash_map<Kmer, Position, hashKmer>, std::string = std::basic_string<char>, Sequence = std::basic_string<char>]’ Aligner.cpp:187:41: instantiated from here Aligner.cpp:94:7: error: variable ‘discarded’ set but not used [-Werror=unused-but-set-variable] cc1plus: all warnings being treated as errors make[2]: *** [libalign_a-Aligner.o] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-biology/abyss-1.2.3/work/abyss-1.2.3/Align' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-biology/abyss-1.2.3/work/abyss-1.2.3' make: *** [all] Error 2 emake failed * ERROR: sci-biology/abyss-1.2.3 failed (compile phase): * emake failed * * Call stack: * ebuild.sh, line 56: Called src_compile * environment, line 355: Called _eapi2_src_compile * ebuild.sh, line 665: Called die * The specific snippet of code: * emake || die "emake failed" * * If you need support, post the output of 'emerge --info =sci-biology/abyss-1.2.3', * the complete build log and the output of 'emerge -pqv =sci-biology/abyss-1.2.3'. * The complete build log is located at '/var/log/portage/build/sci-biology/abyss-1.2.3:20110428-100538.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/abyss-1.2.3/temp/environment'. * S: '/var/tmp/portage/sci-biology/abyss-1.2.3/work/abyss-1.2.3'