- * Package: sci-biology/abyss-1.3.3
- * Repository: gentoo
- * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
- * USE: amd64 elibc_glibc kernel_linux mpi multilib openmp test userland_GNU
- * FEATURES: sandbox test userpriv usersandbox
- >>> Unpacking source...
- >>> Unpacking abyss-1.3.3.tar.gz to /tmp/portage/sci-biology/abyss-1.3.3/work
- >>> Source unpacked in /tmp/portage/sci-biology/abyss-1.3.3/work
- >>> Preparing source in /tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3 ...
- * Running eautoreconf in '/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3' ...
- * Running aclocal ...
- [ ok ]
- * Running autoconf ...
- [ ok ]
- * Running autoheader ...
- [ ok ]
- * Running automake --add-missing --copy --foreign ...
- [ ok ]
- >>> Source prepared.
- >>> Configuring source in /tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3 ...
- ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --disable-dependency-tracking --enable-openmp
- configure: loading site script /usr/share/config.site
- configure: loading site script /usr/share/crossdev/include/site/linux
- configure: loading site script /usr/share/crossdev/include/site/linux-gnu
- configure: loading site script /usr/share/crossdev/include/site/x86_64-linux-gnu
- 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 x86_64-pc-linux-gnu-gcc... x86_64-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 x86_64-pc-linux-gnu-gcc accepts -g... yes
- checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
- checking for style of include used by make... GNU
- checking dependency style of x86_64-pc-linux-gnu-gcc... none
- checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
- checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
- checking whether we are using the GNU C++ compiler... yes
- checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
- checking dependency style of x86_64-pc-linux-gnu-g++... none
- checking for x86_64-pc-linux-gnu-ranlib... x86_64-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
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- 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
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- checking for uint32_t... yes
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- 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... (cached) yes
- checking for working memcmp... yes
- checking for stdlib.h... (cached) yes
- checking for GNU libc compatible realloc... (cached) 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... x86_64-pc-linux-gnu-g++ -E
- 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 for x86_64-pc-linux-gnu-g++ 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 DAssembler/Makefile
- config.status: creating DistanceEst/Makefile
- config.status: creating Map/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 ParseAligns/Makefile
- config.status: creating PathOverlap/Makefile
- config.status: creating Consensus/Makefile
- config.status: creating FilterGraph/Makefile
- config.status: creating config.h
- config.status: executing depfiles commands
- >>> Source configured.
- >>> Compiling source in /tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3 ...
- make -j24
- (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/missing --run autoheader)
- rm -f stamp-h1
- touch config.h.in
- cd . && /bin/sh ./config.status config.h
- config.status: creating config.h
- config.status: config.h is unchanged
- make all-recursive
- make[1]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3'
- Making all in bin
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/bin'
- make[2]: Nothing to be done for `all'.
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/bin'
- Making all in doc
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/doc'
- make[2]: Nothing to be done for `all'.
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/doc'
- Making all in Assembly
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Assembly'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cpp' || echo './'`AssemblyAlgorithms.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-BranchGroup.o `test -f 'BranchGroup.cpp' || echo './'`BranchGroup.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-BranchRecord.o `test -f 'BranchRecord.cpp' || echo './'`BranchRecord.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-DotWriter.o `test -f 'DotWriter.cpp' || echo './'`DotWriter.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-SequenceCollection.o `test -f 'SequenceCollection.cpp' || echo './'`SequenceCollection.cpp
- rm -f libassembly.a
- ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-BranchGroup.o libassembly_a-BranchRecord.o libassembly_a-DotWriter.o libassembly_a-Options.o libassembly_a-SequenceCollection.o
- x86_64-pc-linux-gnu-ranlib libassembly.a
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Assembly'
- Making all in Common
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Common'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-HashFunction.o `test -f 'HashFunction.cpp' || echo './'`HashFunction.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-SeqExt.o `test -f 'SeqExt.cpp' || echo './'`SeqExt.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
- Uncompress.cpp: In function 'int uncompress(const char*)':
- Uncompress.cpp:69:6: warning: variable 'n' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered]
- rm -f libcommon.a
- ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-HashFunction.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-SeqExt.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o
- x86_64-pc-linux-gnu-ranlib libcommon.a
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Common'
- Making all in DataLayer
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DataLayer'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -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
- x86_64-pc-linux-gnu-ranlib libdatalayer.a
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DataLayer'
- Making all in FMIndex
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/FMIndex'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -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
- x86_64-pc-linux-gnu-ranlib libfmindex.a
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/FMIndex'
- Making all in Graph
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Graph'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libgraph_a-ConstrainedSearch.o `test -f 'ConstrainedSearch.cpp' || echo './'`ConstrainedSearch.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc
- rm -f libgraph.a
- ar cru libgraph.a libgraph_a-ConstrainedSearch.o
- x86_64-pc-linux-gnu-ranlib libgraph.a
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -L. -Wl,-O1 -Wl,--as-needed -o abyss-todot abyss_todot-todot.o libgraph.a ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Graph'
- Making all in dialign
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/dialign'
- x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c alig.c
- x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c assemble.c
- x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c diag.c
- x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c io.c
- x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c orf.c
- x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c parameters.c
- x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c prob.c
- x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c translate.c
- x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c museq.c
- io.c: In function 'read_diag_prob_dist':
- io.c:371:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
- io.c: In function 'read_scr_matrix':
- io.c:270:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
- io.c:282:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
- rm -f libdialign.a
- ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o
- x86_64-pc-linux-gnu-ranlib libdialign.a
- x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o dialign museq.o libdialign.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/dialign'
- Making all in Align
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Align'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.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
- x86_64-pc-linux-gnu-ranlib libalign.a
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Align'
- Making all in ABYSS
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/ABYSS'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS-Abyss.o `test -f 'Abyss.cpp' || echo './'`Abyss.cpp
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o ABYSS ABYSS-Abyss.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/ABYSS'
- Making all in Parallel
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Parallel'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -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 -lmpi -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Parallel'
- Making all in AdjList
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/AdjList'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o AdjList AdjList-AdjList.o ../Graph/libgraph.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/AdjList'
- Making all in Consensus
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Consensus'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Consensus'
- Making all in DAssembler
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DAssembler'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DAssembler'
- Making all in DistanceEst
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DistanceEst'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DistanceEst'
- Making all in KAligner
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/KAligner'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -pthread -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -pthread -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -pthread -Wl,-O1 -Wl,--as-needed -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/KAligner'
- Making all in Map
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Map'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Map'
- Making all in MergePaths
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/MergePaths'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o MergeContigs MergeContigs-MergeContigs.o ../DataLayer/libdatalayer.a ../Graph/libgraph.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o PathConsensus PathConsensus-PathConsensus.o ../DataLayer/libdatalayer.a ../Graph/libgraph.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o MergePaths MergePaths-MergePaths.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../Graph/libgraph.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/MergePaths'
- Making all in Overlap
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Overlap'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp
- x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o Overlap Overlap-Overlap.o ../Graph/libgraph.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Overlap'
- Making all in ParseAligns
- make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/ParseAligns'
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
- x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp
- abyss-fixmate.cc:129:8: error: 'intptr_t' does not name a type
- abyss-fixmate.cc: In function 'void printProgress(const Alignments&)':
- abyss-fixmate.cc:142:38: error: expected type-specifier before 'intptr_t'
- abyss-fixmate.cc:142:38: error: expected '>' before 'intptr_t'
- abyss-fixmate.cc:142:38: error: expected '(' before 'intptr_t'
- abyss-fixmate.cc:142:38: error: 'intptr_t' was not declared in this scope
- abyss-fixmate.cc:142:54: error: 'sbrk' was not declared in this scope
- abyss-fixmate.cc:142:59: error: 'sbrk0' was not declared in this scope
- abyss-fixmate.cc:142:64: error: expected ')' before ';' token
- make[2]: *** [abyss_fixmate-abyss-fixmate.o] Error 1
- make[2]: *** Waiting for unfinished jobs....
- make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/ParseAligns'
- make[1]: *** [all-recursive] Error 1
- make[1]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3'
- make: *** [all] Error 2
- * ERROR: sci-biology/abyss-1.3.3 failed (compile phase):
- * emake failed
- *
- * If you need support, post the output of `emerge --info '=sci-biology/abyss-1.3.3'`,
- * the complete build log and the output of `emerge -pqv '=sci-biology/abyss-1.3.3'`.
- * The complete build log is located at '/var/log/portage/sci-biology:abyss-1.3.3:20120620-063015.log'.
- * For convenience, a symlink to the build log is located at '/tmp/portage/sci-biology/abyss-1.3.3/temp/build.log'.
- * The ebuild environment file is located at '/tmp/portage/sci-biology/abyss-1.3.3/temp/environment'.
- * Working directory: '/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3'
- * S: '/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3'