bowtie2 fails to build on certain architectures.
Hello,
Bowtie2 fails to build on number of architectures[0].
I tried to fix this today (see git). But than another problem appears,
for example on armel when I disable -msse2 flag or use -D_NO_SSE2
it fails because of missing emmintrin.h. It is very similar to bug #648803 .
I am wondering if there is a way to solve this problem by tweaking the
Makefile or should it be forwarded to the upstream ?
Thank you,
Alex
[0] https://buildd.debian.org/status/package.php?p=bowtie2
make[1]: Entering directory `/var/cache/pbuilder/pbuilder-mnt/bowtie2-2.0.0-beta5'
/usr/bin/g++ -O3 -D_NO_SSE2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -D_NO_SSE2 -funroll-loops -g3 \"" \
-fno-strict-aliasing -DBOWTIE2_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 -DBOWTIE2 -DNDEBUG -Wall \
\
-o bowtie2-build bt2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp diff_sample.cpp bowtie_build_main.cpp \
ref_read.cpp: In function 'void reverseRefRecords(const EList<RefRecord>&, EList<RefRecord>&, bool, bool)':
ref_read.cpp:223:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'std::pair<unsigned int, unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, int&)':
ref_read.cpp:283:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::printQAlign(std::ostream&, const char*, const BTDnaString&, const EList<Edit>&)':
edit.cpp:100:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:124:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:146:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::printQAlignNoCheck(std::ostream&, const char*, const BTDnaString&, const EList<Edit>&)':
edit.cpp:180:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:201:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:222:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::toRef(const BTDnaString&, const EList<Edit>&, BTDnaString&, bool, size_t, size_t)':
edit.cpp:277:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static bool Edit::repOk(const EList<Edit>&, const BTDnaString&, bool, size_t, size_t)':
edit.cpp:358:8: warning: variable 'del' set but not used [-Wunused-but-set-variable]
edit.cpp:358:21: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:358:34: warning: variable 'mm' set but not used [-Wunused-but-set-variable]
bt2_idx.cpp: In member function 'void Ebwt::countBt2SideRange(SideLocus&, uint32_t, uint32_t*, uint32_t*, EList<bool>*) const':
bt2_idx.cpp:903:7: warning: variable 'adjustedForDollar' set but not used [-Wunused-but-set-variable]
bt2_util.cpp: In member function 'void Ebwt::sanityCheckUpToSide(int) const':
bt2_util.cpp:42:11: warning: variable 'occ_save' set but not used [-Wunused-but-set-variable]
/usr/bin/g++ -O3 -D_NO_SSE2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -D_NO_SSE2 -funroll-loops -g3 \"" \
-fno-strict-aliasing -DBOWTIE2_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 -DBOWTIE2 -DNDEBUG -Wall \
\
-o bowtie2-align bt2_search.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp bowtie_main.cpp \
-lpthread
In file included from bt2_search.cpp:48:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
ref_read.cpp: In function 'void reverseRefRecords(const EList<RefRecord>&, EList<RefRecord>&, bool, bool)':
ref_read.cpp:223:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'std::pair<unsigned int, unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, int&)':
ref_read.cpp:283:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::printQAlign(std::ostream&, const char*, const BTDnaString&, const EList<Edit>&)':
edit.cpp:100:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:124:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:146:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::printQAlignNoCheck(std::ostream&, const char*, const BTDnaString&, const EList<Edit>&)':
edit.cpp:180:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:201:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:222:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::toRef(const BTDnaString&, const EList<Edit>&, BTDnaString&, bool, size_t, size_t)':
edit.cpp:277:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static bool Edit::repOk(const EList<Edit>&, const BTDnaString&, bool, size_t, size_t)':
edit.cpp:358:8: warning: variable 'del' set but not used [-Wunused-but-set-variable]
edit.cpp:358:21: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:358:34: warning: variable 'mm' set but not used [-Wunused-but-set-variable]
bt2_idx.cpp: In member function 'void Ebwt::countBt2SideRange(SideLocus&, uint32_t, uint32_t*, uint32_t*, EList<bool>*) const':
bt2_idx.cpp:903:7: warning: variable 'adjustedForDollar' set but not used [-Wunused-but-set-variable]
bt2_util.cpp: In member function 'void Ebwt::sanityCheckUpToSide(int) const':
bt2_util.cpp:42:11: warning: variable 'occ_save' set but not used [-Wunused-but-set-variable]
reference.cpp: In static member function 'static std::pair<unsigned int, unsigned int> BitPairReference::szsFromFasta(EList<FileBuf*>&, const string&, bool, const RefReadInParams&, EList<RefRecord>&, bool)':
reference.cpp:612:30: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable]
pat.cpp: In member function 'virtual bool FastaPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)':
pat.cpp:747:7: warning: variable 'warning' set but not used [-Wunused-but-set-variable]
read_qseq.cpp: In member function 'virtual bool QseqPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)':
read_qseq.cpp:250:7: warning: variable 'c' set but not used [-Wunused-but-set-variable]
In file included from aligner_sw.cpp:25:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from aligner_sw_driver.h:81:0,
from aligner_sw_driver.cpp:48:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
aligner_result.cpp: In member function 'bool AlnRes::overlap(AlnRes&)':
aligner_result.cpp:328:10: warning: variable 'fivep' set but not used [-Wunused-but-set-variable]
aligner_result.cpp: In member function 'void AlnRes::printCigar(bool, EList<char>&, EList<unsigned int>&, BTString*, char*) const':
aligner_result.cpp:643:8: warning: variable 'printed' set but not used [-Wunused-but-set-variable]
pe.cpp: In member function 'int PairedEndPolicy::peClassifyPair(int64_t, size_t, bool, int64_t, size_t, bool) const':
pe.cpp:130:7: warning: variable 'dovetailing' set but not used [-Wunused-but-set-variable]
aln_sink.cpp: In member function 'void AlnSinkWrap::finishRead(const SeedResults*, const SeedResults*, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, RandomSource&, ReportingMetrics&, const PerReadMetrics&, bool, bool)':
aln_sink.cpp:887:11: warning: variable 'off' set but not used [-Wunused-but-set-variable]
In file included from aligner_swsse.h:28:0,
from aligner_swsse.cpp:22:
sse_util.h:15:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from aligner_swsse_loc_i16.cpp:56:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from aligner_swsse_ee_i16.cpp:56:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from aligner_swsse_loc_u8.cpp:56:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from aligner_swsse_ee_u8.cpp:56:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
make[1]: *** [bowtie2-align] Error 1
make[1]: Leaving directory `/var/cache/pbuilder/pbuilder-mnt/bowtie2-2.0.0-beta5'
dh_auto_build: make -j1 returned exit code 2
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
Reply to: