* Package: sci-biology/abyss-2.0.2-r1  * Repository: gentoo  * Maintainer: sci-biology@gentoo.org haskell@gentoo.org  * USE: abi_x86_64 amd64 elibc_glibc kernel_linux openmp sqlite userland_GNU  * FEATURES: nostrip preserve-libs sandbox splitdebug userpriv usersandbox >>> Unpacking source... >>> Unpacking abyss-2.0.2.tar.gz to /scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work >>> Source unpacked in /scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work >>> Preparing source in /scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 ... * Running eautoreconf in '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2' ... * Running aclocal ...  [ ok ] * Running autoconf --force ...  [ ok ] * Running autoheader ...  [ ok ] * Running automake --add-missing --copy --foreign --force-missing ...  [ ok ] * Running elibtoolize in: abyss-2.0.2/ >>> Source prepared. >>> Configuring source in /scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 ... * econf: updating abyss-2.0.2/config.sub with /usr/share/gnuconfig/config.sub * econf: updating abyss-2.0.2/config.guess with /usr/share/gnuconfig/config.guess ./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 --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/abyss-2.0.2-r1 --htmldir=/usr/share/doc/abyss-2.0.2-r1/html --libdir=/usr/lib64 --enable-openmp --enable-maxk=128 --without-mpi checking for a BSD-compatible install... /usr/lib/portage/python2.7/ebuild-helpers/xattr/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 whether make supports nested variables... 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 whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes 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 x86_64-pc-linux-gnu-ghc... no checking for ghc... (cached) no checking for x86_64-pc-linux-gnu-ghc-pkg... no checking for ghc-pkg... ghc-pkg WARNING: there are broken packages. Run 'ghc-pkg check' for more details. checking for pandoc... yes 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 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... yes checking for std::tr1::hash... yes checking for std::tr1::tuple... 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-pc-linux-gnu checking host system type... x86_64-pc-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... x86_64-pc-linux-gnu-g++ -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... yes checking unordered_map presence... yes checking for unordered_map... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking unordered_set usability... yes checking unordered_set presence... yes checking for unordered_set... yes 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 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 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 >>> Source configured. >>> Compiling source in /scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 ... make -j2 make all-recursive make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2' Making all in bin make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/bin' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/bin' Making all in doc make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/doc' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/doc' Making all in Common make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Common' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 x86_64-pc-linux-gnu-ranlib libcommon.a make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Common' Making all in Graph make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Graph' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 -mpclmul -mpopcnt -march=native -ftree-vectorize -L. -Wl,-O1 -Wl,--as-needed -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Graph' Making all in DataLayer make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataLayer' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataLayer' Making all in DataBase make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataBase' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 x86_64-pc-linux-gnu-ranlib libdb.a x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataBase' Making all in FMIndex make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FMIndex' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 -mpclmul -mpopcnt -march=native -ftree-vectorize -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 -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FMIndex' Making all in Assembly make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Assembly' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 x86_64-pc-linux-gnu-ranlib libassembly.a make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Assembly' Making all in dialign make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/dialign' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o alig.o alig.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o assemble.o assemble.c assemble.c:40:20: warning: inline function 'align_diag' declared but never defined extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); ^~~~~~~~~~ assemble.c:37:32: warning: inline function 'find_eqc' declared but never defined extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); ^~~~~~~~ assemble.c:25:39: warning: inline function 'find_diags_guided' declared but never defined extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, ^~~~~~~~~~~~~~~~~ assemble.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ^~~~~~~~~~~~~~ assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ^~~~~~~~~~~~~~ alig.c:13:20: warning: inline function 'calc_weight' declared but never defined extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o diag.o diag.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o io.o io.c diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); ^~~~~~~~~~~~~~~~ io.c: In function 'read_scr_matrix': io.c:270:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf( fp, "%i", &is); ^~~~~~~~~~~~~~~~~~~~~~ io.c:282:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%s\n", rline); ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'read_diag_prob_dist': io.c:371:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o orf.o orf.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o parameters.o parameters.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o prob.o prob.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o translate.o translate.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 x86_64-pc-linux-gnu-ranlib libdialign.a museq.c: In function 'main': museq.c:168:2: warning: implicit declaration of function 'free_diag' [-Wimplicit-function-declaration] free_diag(adcol.diags[i]); ^~~~~~~~~ museq.c:278:27: warning: implicit declaration of function 'free_alignment' [-Wimplicit-function-declaration] if(! para->FAST_MODE) free_alignment(algn); ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o dialign museq.o libdialign.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/dialign' Making all in Align make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Align' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 x86_64-pc-linux-gnu-ranlib libalign.a x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Align' Making all in ABYSS make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ABYSS' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -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 '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ABYSS' Making all in Parallel make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Parallel' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -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 make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Parallel' Making all in Bloom make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Bloom' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Bloom' Making all in BloomDBG make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/BloomDBG' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/BloomDBG' Making all in Konnector make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Konnector' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Konnector' Making all in Consensus make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Consensus' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Consensus' Making all in DAssembler make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DAssembler' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DAssembler' Making all in DistanceEst make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DistanceEst' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DistanceEst' Making all in KAligner make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/KAligner' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/KAligner' Making all in Layout make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Layout' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Layout' Making all in LogKmerCount make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/LogKmerCount' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/LogKmerCount' Making all in Map make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Map' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 -D SAM_SEQ_QUAL=1 -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_map_ssq-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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -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 x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Map' Making all in MergePaths make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/MergePaths' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -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 make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/MergePaths' Making all in Misc make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Misc' make -O2 -hidir ./ -odir ./ -o abyss-samtobreak samtobreak.hs Usage: make [options] [target] ... Options: -b, -m Ignored for compatibility. -B, --always-make Unconditionally make all targets. -C DIRECTORY, --directory=DIRECTORY Change to DIRECTORY before doing anything. -d Print lots of debugging information. --debug[=FLAGS] Print various types of debugging information. -e, --environment-overrides Environment variables override makefiles. --eval=STRING Evaluate STRING as a makefile statement. -f FILE, --file=FILE, --makefile=FILE Read FILE as a makefile. -h, --help Print this message and exit. -i, --ignore-errors Ignore errors from recipes. -I DIRECTORY, --include-dir=DIRECTORY Search DIRECTORY for included makefiles. -j [N], --jobs[=N] Allow N jobs at once; infinite jobs with no arg. -k, --keep-going Keep going when some targets can't be made. -l [N], --load-average[=N], --max-load[=N] Don't start multiple jobs unless load is below N. -L, --check-symlink-times Use the latest mtime between symlinks and target. -n, --just-print, --dry-run, --recon Don't actually run any recipe; just print them. -o FILE, --old-file=FILE, --assume-old=FILE Consider FILE to be very old and don't remake it. -O[TYPE], --output-sync[=TYPE] Synchronize output of parallel jobs by TYPE. -p, --print-data-base Print make's internal database. -q, --question Run no recipe; exit status says if up to date. -r, --no-builtin-rules Disable the built-in implicit rules. -R, --no-builtin-variables Disable the built-in variable settings. -s, --silent, --quiet Don't echo recipes. -S, --no-keep-going, --stop Turns off -k. -t, --touch Touch targets instead of remaking them. --trace Print tracing information. -v, --version Print the version number of make and exit. -w, --print-directory Print the current directory. --no-print-directory Turn off -w, even if it was turned on implicitly. -W FILE, --what-if=FILE, --new-file=FILE, --assume-new=FILE Consider FILE to be infinitely new. --warn-undefined-variables Warn when an undefined variable is referenced. This program built for x86_64-pc-linux-gnu Report bugs to make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Misc' Making all in Overlap make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Overlap' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Overlap' Making all in PairedDBG make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PairedDBG' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o KmerPair.o KmerPair.cc x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc rm -f libpaireddbg.a ar cru libpaireddbg.a KmerPair.o x86_64-pc-linux-gnu-ranlib libpaireddbg.a x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -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 '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PairedDBG' Making all in ParseAligns make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ParseAligns' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -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 -D SAM_SEQ_QUAL=1 -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc abyss-fixmate.cc: In function 'void handleAlignment(SAMRecord&, Alignments&)': abyss-fixmate.cc:213:27: warning: 'void boost::unordered::unordered_map::quick_erase(boost::unordered::unordered_map::const_iterator) [with K = std::__cxx11::basic_string; T = SAMAlignment; H = boost::hash >; P = std::equal_to >; A = std::allocator, SAMAlignment> >; boost::unordered::unordered_map::const_iterator = boost::unordered::iterator_detail::c_iterator, SAMAlignment> > >]' is deprecated: Use erase instead [-Wdeprecated-declarations] map.quick_erase(it.first); ^ In file included from /usr/include/boost/unordered_map.hpp:17:0, from abyss-fixmate.cc:17: /usr/include/boost/unordered/unordered_map.hpp:723:10: note: declared here void quick_erase(const_iterator it) { erase(it); } ^~~~~~~~~~~ abyss-fixmate.cc: In function 'void handleAlignment(SAMRecord&, Alignments&)': abyss-fixmate.cc:213:27: warning: 'void boost::unordered::unordered_map::quick_erase(boost::unordered::unordered_map::const_iterator) [with K = std::__cxx11::basic_string; T = SAMRecord; H = boost::hash >; P = std::equal_to >; A = std::allocator, SAMRecord> >; boost::unordered::unordered_map::const_iterator = boost::unordered::iterator_detail::c_iterator, SAMRecord> > >]' is deprecated: Use erase instead [-Wdeprecated-declarations] map.quick_erase(it.first); ^ In file included from /usr/include/boost/unordered_map.hpp:17:0, from abyss-fixmate.cc:17: /usr/include/boost/unordered/unordered_map.hpp:723:10: note: declared here void quick_erase(const_iterator it) { erase(it); } ^~~~~~~~~~~ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ParseAligns' Making all in PathOverlap make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PathOverlap' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PathOverlap' Making all in PopBubbles make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PopBubbles' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PopBubbles' Making all in Scaffold make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Scaffold' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Scaffold' Making all in SimpleGraph make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/SimpleGraph' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -Wno-strict-aliasing -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -Wno-strict-aliasing -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/SimpleGraph' Making all in kmerprint make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/kmerprint' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/kmerprint' Making all in FilterGraph make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FilterGraph' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FilterGraph' Making all in GapFiller make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/GapFiller' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -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 '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/GapFiller' Making all in Sealer make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Sealer' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc pandoc -s -o abyss-sealer.1 README.md x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Sealer' Making all in AdjList make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/AdjList' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2 -isystem/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/boost_1_56_0 -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed -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 '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/AdjList' Making all in lib/bloomfilter make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/bloomfilter' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/bloomfilter' Making all in lib/rolling-hash make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/rolling-hash' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/rolling-hash' Making all in lib/gtest-1.7.0 make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/gtest-1.7.0' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/gtest-1.7.0' Making all in Unittest make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Unittest' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Unittest' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2' pandoc -s -o README.html README.md make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2' >>> Source compiled. >>> Test phase [not enabled]: sci-biology/abyss-2.0.2-r1 >>> Install abyss-2.0.2-r1 into /scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image/ category sci-biology make -j2 DESTDIR=/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image/ install Making install in bin make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/bin' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/bin' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/bin' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/bin' Making install in doc make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/doc' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/doc' make[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/share/doc/abyss-2.0.2-r1' /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/share/man/man1' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/share/doc/abyss-2.0.2-r1' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/share/man/man1' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/doc' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/doc' Making install in Common make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Common' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Common' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Common' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Common' Making install in Graph make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Graph' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Graph' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-gc abyss-todot '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Graph' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Graph' Making install in DataLayer make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataLayer' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataLayer' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-fac abyss-tofastq '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataLayer' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataLayer' Making install in DataBase make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataBase' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataBase' /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-db-txt '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-db-csv '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataBase' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DataBase' Making install in FMIndex make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FMIndex' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FMIndex' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FMIndex' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FMIndex' Making install in Assembly make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Assembly' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Assembly' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Assembly' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Assembly' Making install in dialign make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/dialign' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/dialign' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/dialign' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/dialign' Making install in Align make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Align' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Align' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-align abyss-mergepairs '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Align' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Align' Making install in ABYSS make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ABYSS' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ABYSS' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c ABYSS '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ABYSS' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ABYSS' Making install in Parallel make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Parallel' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Parallel' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c ABYSS-P abyss-paired-dbg-mpi '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Parallel' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Parallel' Making install in Bloom make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Bloom' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Bloom' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-bloom '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Bloom' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Bloom' Making install in BloomDBG make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/BloomDBG' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/BloomDBG' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-bloom-dbg '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/BloomDBG' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/BloomDBG' Making install in Konnector make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Konnector' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Konnector' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c konnector '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Konnector' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Konnector' Making install in Consensus make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Consensus' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Consensus' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c Consensus '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Consensus' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Consensus' Making install in DAssembler make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DAssembler' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DAssembler' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c DAssembler '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DAssembler' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DAssembler' Making install in DistanceEst make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DistanceEst' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DistanceEst' /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Nothing to be done for 'install-data-am'. /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c DistanceEst DistanceEst-ssq '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DistanceEst' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/DistanceEst' Making install in KAligner make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/KAligner' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/KAligner' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c KAligner '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/KAligner' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/KAligner' Making install in Layout make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Layout' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Layout' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-layout '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Layout' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Layout' Making install in LogKmerCount make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/LogKmerCount' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/LogKmerCount' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c logcounter '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/LogKmerCount' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/LogKmerCount' Making install in Map make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Map' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Map' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Map' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Map' Making install in MergePaths make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/MergePaths' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/MergePaths' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c MergePaths MergeContigs PathConsensus '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/MergePaths' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/MergePaths' Making install in Misc make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Misc' make -O2 -hidir ./ -odir ./ -o abyss-samtobreak samtobreak.hs Usage: make [options] [target] ... Options: -b, -m Ignored for compatibility. -B, --always-make Unconditionally make all targets. -C DIRECTORY, --directory=DIRECTORY Change to DIRECTORY before doing anything. -d Print lots of debugging information. --debug[=FLAGS] Print various types of debugging information. -e, --environment-overrides Environment variables override makefiles. --eval=STRING Evaluate STRING as a makefile statement. -f FILE, --file=FILE, --makefile=FILE Read FILE as a makefile. -h, --help Print this message and exit. -i, --ignore-errors Ignore errors from recipes. -I DIRECTORY, --include-dir=DIRECTORY Search DIRECTORY for included makefiles. -j [N], --jobs[=N] Allow N jobs at once; infinite jobs with no arg. -k, --keep-going Keep going when some targets can't be made. -l [N], --load-average[=N], --max-load[=N] Don't start multiple jobs unless load is below N. -L, --check-symlink-times Use the latest mtime between symlinks and target. -n, --just-print, --dry-run, --recon Don't actually run any recipe; just print them. -o FILE, --old-file=FILE, --assume-old=FILE Consider FILE to be very old and don't remake it. -O[TYPE], --output-sync[=TYPE] Synchronize output of parallel jobs by TYPE. -p, --print-data-base Print make's internal database. -q, --question Run no recipe; exit status says if up to date. -r, --no-builtin-rules Disable the built-in implicit rules. -R, --no-builtin-variables Disable the built-in variable settings. -s, --silent, --quiet Don't echo recipes. -S, --no-keep-going, --stop Turns off -k. -t, --touch Touch targets instead of remaking them. --trace Print tracing information. -v, --version Print the version number of make and exit. -w, --print-directory Print the current directory. --no-print-directory Turn off -w, even if it was turned on implicitly. -W FILE, --what-if=FILE, --new-file=FILE, --assume-new=FILE Consider FILE to be infinitely new. --warn-undefined-variables Warn when an undefined variable is referenced. This program built for x86_64-pc-linux-gnu Report bugs to make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Misc' make -O2 -hidir ./ -odir ./ -o abyss-samtobreak samtobreak.hs Usage: make [options] [target] ... make[2]: Nothing to be done for 'install-data-am'. Options: -b, -m Ignored for compatibility. -B, --always-make Unconditionally make all targets. -C DIRECTORY, --directory=DIRECTORY Change to DIRECTORY before doing anything. -d Print lots of debugging information. --debug[=FLAGS] Print various types of debugging information. -e, --environment-overrides Environment variables override makefiles. --eval=STRING Evaluate STRING as a makefile statement. -f FILE, --file=FILE, --makefile=FILE Read FILE as a makefile. -h, --help Print this message and exit. -i, --ignore-errors Ignore errors from recipes. -I DIRECTORY, --include-dir=DIRECTORY Search DIRECTORY for included makefiles. -j [N], --jobs[=N] Allow N jobs at once; infinite jobs with no arg. -k, --keep-going Keep going when some targets can't be made. -l [N], --load-average[=N], --max-load[=N] Don't start multiple jobs unless load is below N. -L, --check-symlink-times Use the latest mtime between symlinks and target. -n, --just-print, --dry-run, --recon Don't actually run any recipe; just print them. -o FILE, --old-file=FILE, --assume-old=FILE Consider FILE to be very old and don't remake it. -O[TYPE], --output-sync[=TYPE] Synchronize output of parallel jobs by TYPE. -p, --print-data-base Print make's internal database. -q, --question Run no recipe; exit status says if up to date. -r, --no-builtin-rules Disable the built-in implicit rules. -R, --no-builtin-variables Disable the built-in variable settings. -s, --silent, --quiet Don't echo recipes. -S, --no-keep-going, --stop Turns off -k. -t, --touch Touch targets instead of remaking them. --trace Print tracing information. -v, --version Print the version number of make and exit. -w, --print-directory Print the current directory. --no-print-directory Turn off -w, even if it was turned on implicitly. -W FILE, --what-if=FILE, --new-file=FILE, --assume-new=FILE Consider FILE to be infinitely new. --warn-undefined-variables Warn when an undefined variable is referenced. This program built for x86_64-pc-linux-gnu Report bugs to /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Misc' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Misc' Making install in Overlap make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Overlap' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Overlap' /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Nothing to be done for 'install-data-am'. /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c Overlap '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Overlap' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Overlap' Making install in PairedDBG make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PairedDBG' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PairedDBG' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-paired-dbg '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PairedDBG' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PairedDBG' Making install in ParseAligns make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ParseAligns' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ParseAligns' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ParseAligns' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/ParseAligns' Making install in PathOverlap make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PathOverlap' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PathOverlap' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c PathOverlap '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PathOverlap' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PathOverlap' Making install in PopBubbles make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PopBubbles' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PopBubbles' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c PopBubbles '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PopBubbles' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/PopBubbles' Making install in Scaffold make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Scaffold' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Scaffold' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-scaffold abyss-junction abyss-longseqdist '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Scaffold' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Scaffold' Making install in SimpleGraph make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/SimpleGraph' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/SimpleGraph' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c SimpleGraph '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/SimpleGraph' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/SimpleGraph' Making install in kmerprint make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/kmerprint' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/kmerprint' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/kmerprint' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/kmerprint' Making install in FilterGraph make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FilterGraph' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FilterGraph' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-filtergraph '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FilterGraph' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/FilterGraph' Making install in GapFiller make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/GapFiller' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/GapFiller' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-gapfill '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/GapFiller' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/GapFiller' Making install in Sealer make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Sealer' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Sealer' /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/share/man/man1' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c -m 644 abyss-sealer.1 '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/share/man/man1' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c abyss-sealer '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Sealer' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Sealer' Making install in AdjList make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/AdjList' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/AdjList' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c AdjList '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/bin' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/AdjList' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/AdjList' Making install in lib/bloomfilter make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/bloomfilter' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/bloomfilter' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/bloomfilter' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/bloomfilter' Making install in lib/rolling-hash make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/rolling-hash' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/rolling-hash' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/rolling-hash' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/rolling-hash' Making install in lib/gtest-1.7.0 make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/gtest-1.7.0' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/gtest-1.7.0' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/gtest-1.7.0' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/lib/gtest-1.7.0' Making install in Unittest make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Unittest' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Unittest' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Unittest' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Unittest' make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2' make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2' make[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/share/doc/abyss-2.0.2-r1' /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md README.html '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image//usr/share/doc/abyss-2.0.2-r1' make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2' make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2' >>> Completed installing abyss-2.0.2-r1 into /scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/image/ * Final size of build directory: 27780 KiB (27.1 MiB) * Final size of installed tree: 8616 KiB ( 8.4 MiB) ecompressdir: bzip2 -9 /usr/share/man ecompressdir: bzip2 -9 /usr/share/doc