Build log

abyss-1.2.3:20110428-100538.log (text/plain), 9.08 KB, created by Diego Elio Pettenò (RETIRED) on 2011-04-28 13:15:31 UTC

 * Package:    sci-biology/abyss-1.2.3
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * 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'