build.log

build.log (text/plain), 111.00 KB, created by Martin Mokrejš on 2018-02-03 11:28:38 UTC

[32;01m * [39;49;00mPackage:    sci-biology/abyss-2.0.2-r1
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail] [e-mail]
[32;01m * [39;49;00mUSE:        abi_x86_64 amd64 elibc_glibc kernel_linux openmp sqlite userland_GNU
[32;01m * [39;49;00mFEATURES:   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 ...
 [32;01m*[0m Running eautoreconf in '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2' ...
 [32;01m*[0m Running aclocal ...
[A[229C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf --force ...
[A[229C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoheader ...
[A[229C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy --foreign --force-missing ...
[A[229C [34;01m[ [32;01mok[34;01m ][0m
 * 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<int>... yes
checking for std::tr1::hash<int>... yes
checking for std::tr1::tuple<int>... yes
checking for dup2... yes
checking for gethostname... yes
checking for getopt_long... yes
checking for getpagesize... yes
checking for memset... yes
checking for strdup... yes
checking for strerror... yes
checking for strtoul... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking whether HOST_NAME_MAX is declared... yes
checking build system type... x86_64-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
[01m[Kassemble.c:40:20:[m[K [01;35m[Kwarning: [m[Kinline function '[01m[Kalign_diag[m[K' declared but never defined
 extern inline char [01;35m[Kalign_diag[m[K(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
                    [01;35m[K^~~~~~~~~~[m[K
[01m[Kassemble.c:37:32:[m[K [01;35m[Kwarning: [m[Kinline function '[01m[Kfind_eqc[m[K' declared but never defined
 extern inline struct algn_pos *[01;35m[Kfind_eqc[m[K(struct algn_pos **ap, int seqnum, int pos);
                                [01;35m[K^~~~~~~~[m[K
[01m[Kassemble.c:25:39:[m[K [01;35m[Kwarning: [m[Kinline function '[01m[Kfind_diags_guided[m[K' declared but never defined
 extern inline struct simple_diag_col* [01;35m[Kfind_diags_guided[m[K(struct scr_matrix *smatrix,
                                       [01;35m[K^~~~~~~~~~~~~~~~~[m[K
[01m[Kassemble.c:15:20:[m[K [01;35m[Kwarning: [m[Kinline function '[01m[Kcalc_ov_weight[m[K' declared but never defined
 extern inline void [01;35m[Kcalc_ov_weight[m[K(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
                    [01;35m[K^~~~~~~~~~~~~~[m[K
[01m[Kassemble.c:13:20:[m[K [01;35m[Kwarning: [m[Kinline function '[01m[Kcalc_weight[m[K' declared but never defined
 extern inline void [01;35m[Kcalc_weight[m[K(struct diag* dg, struct scr_matrix* smatrix,
                    [01;35m[K^~~~~~~~~~~[m[K
[01m[Kalig.c:15:20:[m[K [01;35m[Kwarning: [m[Kinline function '[01m[Kcalc_ov_weight[m[K' declared but never defined
 extern inline void [01;35m[Kcalc_ov_weight[m[K(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
                    [01;35m[K^~~~~~~~~~~~~~[m[K
[01m[Kalig.c:13:20:[m[K [01;35m[Kwarning: [m[Kinline function '[01m[Kcalc_weight[m[K' declared but never defined
 extern inline void [01;35m[Kcalc_weight[m[K(struct diag* dg, struct scr_matrix* smatrix,
                    [01;35m[K^~~~~~~~~~~[m[K
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
[01m[Kdiag.c:1456:3:[m[K [01;35m[Kwarning: [m[K'[01m[Kreal_calc_weight[m[K' is static but used in inline function '[01m[Kfind_diags_dyn[m[K' which is not static
   [01;35m[Kreal_calc_weight[m[K(dg, smatrix, pdist,1,tmp_dist,algn);
   [01;35m[K^~~~~~~~~~~~~~~~[m[K
[01m[Kio.c:[m[K In function '[01m[Kread_scr_matrix[m[K':
[01m[Kio.c:270:3:[m[K [01;35m[Kwarning: [m[Kignoring return value of '[01m[Kfscanf[m[K', declared with attribute warn_unused_result [[01;35m[K-Wunused-result[m[K]
   [01;35m[Kfscanf( fp, "%i", &is)[m[K;
   [01;35m[K^~~~~~~~~~~~~~~~~~~~~~[m[K
[01m[Kio.c:282:5:[m[K [01;35m[Kwarning: [m[Kignoring return value of '[01m[Kfscanf[m[K', declared with attribute warn_unused_result [[01;35m[K-Wunused-result[m[K]
     [01;35m[Kfscanf(fp, "%s\n", rline)[m[K;
     [01;35m[K^~~~~~~~~~~~~~~~~~~~~~~~~[m[K
[01m[Kio.c:[m[K In function '[01m[Kread_diag_prob_dist[m[K':
[01m[Kio.c:371:7:[m[K [01;35m[Kwarning: [m[Kignoring return value of '[01m[Kfscanf[m[K', declared with attribute warn_unused_result [[01;35m[K-Wunused-result[m[K]
       [01;35m[Kfscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight )[m[K;
       [01;35m[K^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~[m[K
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
[01m[Kmuseq.c:[m[K In function '[01m[Kmain[m[K':
[01m[Kmuseq.c:168:2:[m[K [01;35m[Kwarning: [m[Kimplicit declaration of function '[01m[Kfree_diag[m[K' [[01;35m[K-Wimplicit-function-declaration[m[K]
  [01;35m[Kfree_diag[m[K(adcol.diags[i]);
  [01;35m[K^~~~~~~~~[m[K
[01m[Kmuseq.c:278:27:[m[K [01;35m[Kwarning: [m[Kimplicit declaration of function '[01m[Kfree_alignment[m[K' [[01;35m[K-Wimplicit-function-declaration[m[K]
     if(! para->FAST_MODE) [01;35m[Kfree_alignment[m[K(algn);
                           [01;35m[K^~~~~~~~~~~~~~[m[K
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 <[e-mail]>
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
[01m[Kabyss-fixmate.cc:[m[K In function '[01m[Kvoid handleAlignment(SAMRecord&, Alignments&)[m[K':
[01m[Kabyss-fixmate.cc:213:27:[m[K [01;35m[Kwarning: [m[K'[01m[Kvoid boost::unordered::unordered_map<K, T, H, P, A>::quick_erase(boost::unordered::unordered_map<K, T, H, P, A>::const_iterator) [with K = std::__cxx11::basic_string<char>; T = SAMAlignment; H = boost::hash<std::__cxx11::basic_string<char> >; P = std::equal_to<std::__cxx11::basic_string<char> >; A = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SAMAlignment> >; boost::unordered::unordered_map<K, T, H, P, A>::const_iterator = boost::unordered::iterator_detail::c_iterator<boost::unordered::detail::ptr_node<std::pair<const std::__cxx11::basic_string<char>, SAMAlignment> > >][m[K' is deprecated: Use erase instead [[01;35m[K-Wdeprecated-declarations[m[K]
   map.quick_erase(it.first[01;35m[K)[m[K;
                           [01;35m[K^[m[K
In file included from [01m[K/usr/include/boost/unordered_map.hpp:17:0[m[K,
                 from [01m[Kabyss-fixmate.cc:17[m[K:
[01m[K/usr/include/boost/unordered/unordered_map.hpp:723:10:[m[K [01;36m[Knote: [m[Kdeclared here
     void [01;36m[Kquick_erase[m[K(const_iterator it) { erase(it); }
          [01;36m[K^~~~~~~~~~~[m[K
[01m[Kabyss-fixmate.cc:[m[K In function '[01m[Kvoid handleAlignment(SAMRecord&, Alignments&)[m[K':
[01m[Kabyss-fixmate.cc:213:27:[m[K [01;35m[Kwarning: [m[K'[01m[Kvoid boost::unordered::unordered_map<K, T, H, P, A>::quick_erase(boost::unordered::unordered_map<K, T, H, P, A>::const_iterator) [with K = std::__cxx11::basic_string<char>; T = SAMRecord; H = boost::hash<std::__cxx11::basic_string<char> >; P = std::equal_to<std::__cxx11::basic_string<char> >; A = std::allocator<std::pair<const std::__cxx11::basic_string<char>, SAMRecord> >; boost::unordered::unordered_map<K, T, H, P, A>::const_iterator = boost::unordered::iterator_detail::c_iterator<boost::unordered::detail::ptr_node<std::pair<const std::__cxx11::basic_string<char>, SAMRecord> > >][m[K' is deprecated: Use erase instead [[01;35m[K-Wdeprecated-declarations[m[K]
   map.quick_erase(it.first[01;35m[K)[m[K;
                           [01;35m[K^[m[K
In file included from [01m[K/usr/include/boost/unordered_map.hpp:17:0[m[K,
                 from [01m[Kabyss-fixmate.cc:17[m[K:
[01m[K/usr/include/boost/unordered/unordered_map.hpp:723:10:[m[K [01;36m[Knote: [m[Kdeclared here
     void [01;36m[Kquick_erase[m[K(const_iterator it) { erase(it); }
          [01;36m[K^~~~~~~~~~~[m[K
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 <[e-mail]>
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 <[e-mail]>
 /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/

 [32;01m*[0m Final size of build directory: 27780 KiB (27.1 MiB)
 [32;01m*[0m Final size of installed tree:   8616 KiB ( 8.4 MiB)

ecompressdir: bzip2 -9 /usr/share/man
ecompressdir: bzip2 -9 /usr/share/doc