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Gentoo's Bugzilla – Attachment 247398 Details for
Bug 337426
sci-biology/bowtie does not respect LDFLAGS
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Build log
bowtie-0.12.5:20100914-233326.log (text/plain), 5.61 KB, created by
Diego Elio Pettenò (RETIRED)
on 2010-09-15 07:00:07 UTC
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Description:
Build log
Filename:
MIME Type:
Creator:
Diego Elio Pettenò (RETIRED)
Created:
2010-09-15 07:00:07 UTC
Size:
5.61 KB
patch
obsolete
> * 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 >
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bug 337426
: 247398