* CPV:  sci-biology/bowtie-0.12.5
 * REPO: gentoo
 * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
 * USE:  elibc_glibc kernel_linux test userland_GNU x86
>>> Unpacking source...
>>> Unpacking bowtie-0.12.5-src.zip to /var/tmp/portage/sci-biology/bowtie-0.12.5/work
>>> Source unpacked in /var/tmp/portage/sci-biology/bowtie-0.12.5/work
>>> Preparing source in /var/tmp/portage/sci-biology/bowtie-0.12.5/work/bowtie-0.12.5 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/bowtie-0.12.5/work/bowtie-0.12.5 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/bowtie-0.12.5/work/bowtie-0.12.5 ...
make -j14 
cat ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp pool.h filebuf.h hit.h random_source.h assert_helpers.h ebwt_search_util.h diff_sample.h range_cache.h range_chaser.h ebwt.h log.h refmap.h blockwise_sa.h range.h endian_swap.h ref_aligner.h mm.h hit_set.h pat.h color_dec.h bitpack.h spinlock.h zbox.h aligner.h sam.h reference.h aligner_metrics.h range_source.h auto_array.h word_io.h sequence_io.h aligner_1mm.h alphabet.h qual.h binary_sa_search.h threading.h row_chaser.h ref_read.h aligner_23mm.h color.h annot.h timer.h aligner_0mm.h str_util.h tokenize.h multikey_qsort.h formats.h ebwt_search_backtrack.h shmem.h search_globals.h edit.h aligner_seed_mm.h bitset.h | md5sum | awk '{print $1}' > .bowtie-build.md5
/usr/bin/g++ -O2 -pipe -O3  -DCOMPILER_OPTIONS="\"-O3  \""  \
	-DEBWT_BUILD_HASH=`cat .bowtie-build.md5` \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM  -DNDEBUG -Wall \
	-I SeqAn-1.1 \
	-o bowtie-build ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp  bowtie_build_main.cpp \
	 
cat ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp pool.h filebuf.h hit.h random_source.h assert_helpers.h ebwt_search_util.h diff_sample.h range_cache.h range_chaser.h ebwt.h log.h refmap.h blockwise_sa.h range.h endian_swap.h ref_aligner.h mm.h hit_set.h pat.h color_dec.h bitpack.h spinlock.h zbox.h aligner.h sam.h reference.h aligner_metrics.h range_source.h auto_array.h word_io.h sequence_io.h aligner_1mm.h alphabet.h qual.h binary_sa_search.h threading.h row_chaser.h ref_read.h aligner_23mm.h color.h annot.h timer.h aligner_0mm.h str_util.h tokenize.h multikey_qsort.h formats.h ebwt_search_backtrack.h shmem.h search_globals.h edit.h aligner_seed_mm.h bitset.h search_23mm_phase1.c search_1mm_phase2.c search_seeded_phase3.c search_23mm_phase3.c search_23mm_phase2.c search_1mm_phase1.c search_seeded_phase2.c search_seeded_phase4.c search_seeded_phase1.c | md5sum | awk '{print $1}' > .bowtie.md5
/usr/bin/g++ -O2 -pipe -O3  -DCOMPILER_OPTIONS="\"-O3  \""  \
	-DEBWT_SEARCH_HASH=`cat .bowtie.md5` \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM  -DNDEBUG -Wall \
	-I SeqAn-1.1 \
	-o bowtie ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
	 -lpthread
cat bowtie_inspect.cpp pool.h filebuf.h hit.h random_source.h assert_helpers.h ebwt_search_util.h diff_sample.h range_cache.h range_chaser.h ebwt.h log.h refmap.h blockwise_sa.h range.h endian_swap.h ref_aligner.h mm.h hit_set.h pat.h color_dec.h bitpack.h spinlock.h zbox.h aligner.h sam.h reference.h aligner_metrics.h range_source.h auto_array.h word_io.h sequence_io.h aligner_1mm.h alphabet.h qual.h binary_sa_search.h threading.h row_chaser.h ref_read.h aligner_23mm.h color.h annot.h timer.h aligner_0mm.h str_util.h tokenize.h multikey_qsort.h formats.h ebwt_search_backtrack.h shmem.h search_globals.h edit.h aligner_seed_mm.h bitset.h ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp | md5sum | awk '{print $1}' > .bowtie-inspect.md5
/usr/bin/g++ -O2 -pipe -O3  \
	-DCOMPILER_OPTIONS="\"-O3  \""  \
	-DEBWT_INSPECT_HASH=`cat .bowtie-inspect.md5` \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM  -Wall \
	-I SeqAn-1.1 -I . \
	-o bowtie-inspect bowtie_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp \
	
>>> Source compiled.
>>> Test phase [none]: sci-biology/bowtie-0.12.5

>>> Install bowtie-0.12.5 into /var/tmp/portage/sci-biology/bowtie-0.12.5/image/ category sci-biology
doexe: warning, skipping directory scripts/test.pl
>>> Completed installing bowtie-0.12.5 into /var/tmp/portage/sci-biology/bowtie-0.12.5/image/

strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment
   usr/bin/bowtie-inspect
   usr/bin/bowtie
   usr/bin/bowtie-build

 * QA Notice: Files built without respecting LDFLAGS have been detected
 *  Please include the following list of files in your report:
 * /usr/bin/bowtie-inspect
 * /usr/bin/bowtie
 * /usr/bin/bowtie-build