sci-biology:bowtie-0.12.8:20151028-020235.log

sci-biology:bowtie-0.12.8:20151028-020235.log (text/plain), 34.57 KB, created by Toralf Förster on 2015-10-28 12:53:48 UTC

 * Package:    sci-biology/bowtie-0.12.8
 * Repository: gentoo
 * Maintainer: sci-biology
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux policykit userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking bowtie-0.12.8-src.zip to /var/tmp/portage/sci-biology/bowtie-0.12.8/work
>>> Source unpacked in /var/tmp/portage/sci-biology/bowtie-0.12.8/work
>>> Preparing source in /var/tmp/portage/sci-biology/bowtie-0.12.8/work/bowtie-0.12.8 ...
 * Applying bowtie-0.12.8-gcc-47.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/bowtie-0.12.8/work/bowtie-0.12.8 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/bowtie-0.12.8/work/bowtie-0.12.8 ...
make -j1 CC=x86_64-pc-linux-gnu-gcc CPP=x86_64-pc-linux-gnu-g++ CXX=x86_64-pc-linux-gnu-g++ 'EXTRA_FLAGS=-Wl,-O1 -Wl,--as-needed' RELEASE_FLAGS= 
cat ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp filebuf.h bitset.h hit.h assert_helpers.h range_cache.h range_chaser.h pool.h log.h ebwt.h aligner_0mm.h blockwise_sa.h aligner_23mm.h range.h endian_swap.h mm.h hit_set.h binary_sa_search.h pat.h color_dec.h ebwt_search_backtrack.h aligner_seed_mm.h spinlock.h ebwt_search_util.h zbox.h aligner.h sam.h reference.h ref_aligner.h multikey_qsort.h word_io.h range_source.h diff_sample.h annot.h alphabet.h auto_array.h sequence_io.h row_chaser.h ref_read.h color.h refmap.h threading.h random_source.h timer.h str_util.h shmem.h bitpack.h formats.h tokenize.h search_globals.h qual.h edit.h aligner_1mm.h aligner_metrics.h | md5sum | awk '{print $1}' > .bowtie-build.md5
x86_64-pc-linux-gnu-g++  -DCOMPILER_OPTIONS="\" -Wl,-O1 -Wl,--as-needed  -march=native -O2 -pipe \"" -Wl,-O1 -Wl,--as-needed  -march=native -O2 -pipe  \
	-DEBWT_BUILD_HASH=`cat .bowtie-build.md5` \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`x86_64-pc-linux-gnu-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 \
	 
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)’:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’:
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’:
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)’:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’:
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/index.h:82:0,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)’:
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)’:
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
                                                                 ^
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
                                                                ^
SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)’:
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)’:
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function ‘typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)’:
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
In file included from SeqAn-1.1/seqan/index.h:83:0,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)’:
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)’:
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
 ypedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                        ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function ‘typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)’:
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
 ypedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                        ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from ebwt_build.cpp:7:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)’:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from ebwt_build.cpp:7:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)’:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from ebwt.h:27:0,
                 from ebwt_build.cpp:11:
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::buildSamples()’:
blockwise_sa.h:380:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
blockwise_sa.h: In member function ‘virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()’:
blockwise_sa.h:745:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from ebwt.h:1607:0,
                 from ebwt_build.cpp:11:
ebwt_search_backtrack.h: In member function ‘bool GreedyDFSRangeSource::backtrack(uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t*, uint8_t*, bool)’:
ebwt_search_backtrack.h:772:11: warning: variable ‘foundTarget’ set but not used [-Wunused-but-set-variable]
      bool foundTarget = false;
           ^
In file included from ebwt_build.cpp:11:0:
ebwt.h: At global scope:
ebwt.h:3948:19: error: redeclaration of ‘void Ebwt<TStr>::joinToDisk(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, TStr&, std::ostream&, std::ostream&, uint32_t)’ may not have default arguments [-fpermissive]
  uint32_t seed = 0)
                   ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of ‘struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >’:
SeqAn-1.1/seqan/sequence/string_packed.h:906:102:   required from ‘typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]’
SeqAn-1.1/seqan/sequence/string_packed.h:1237:40:   required from ‘typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]’
SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from ‘typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]’
blockwise_sa.h:354:32:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between ‘enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>’ and ‘enum seqan::BitsPerValue<unsigned int>::<anonymous>’ [-Wenum-compare]
   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST
                                     ^
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of ‘struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >’:
SeqAn-1.1/seqan/sequence/string_packed.h:731:88:   required from ‘typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Alloc<void>; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]’
ebwt.h:3901:32:   required from ‘static TStr Ebwt<TStr>::join(std::vector<FileBuf*>&, std::vector<RefRecord>&, uint32_t, const RefReadInParams&, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; uint32_t = unsigned int]’
ebwt_build.cpp:463:9:   required from ‘void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::string = std::basic_string<char>]’
ebwt_build.cpp:600:69:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between ‘enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>’ and ‘enum seqan::BitsPerValue<unsigned int>::<anonymous>’ [-Wenum-compare]
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)’:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’:
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’:
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)’:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’:
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)’:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)’:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
ref_read.cpp: In function ‘void reverseRefRecords(const std::vector<RefRecord>&, std::vector<RefRecord>&, bool, bool)’:
ref_read.cpp:195:8: warning: variable ‘mergedLast’ set but not used [-Wunused-but-set-variable]
   bool mergedLast;
        ^
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadSizes(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, const RefReadInParams&, BitpairOutFileBuf*, int&)’:
ref_read.cpp:243:18: warning: variable ‘rpcp’ set but not used [-Wunused-but-set-variable]
  RefReadInParams rpcp = rparms;
                  ^
Makefile:189: recipe for target 'bowtie-build' failed
make: *** [bowtie-build] Error 1
 * ERROR: sci-biology/bowtie-0.12.8::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/bowtie-0.12.8::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/bowtie-0.12.8::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:bowtie-0.12.8:20151028-020235.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/bowtie-0.12.8/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/bowtie-0.12.8/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/bowtie-0.12.8/work/bowtie-0.12.8'
 * S: '/var/tmp/portage/sci-biology/bowtie-0.12.8/work/bowtie-0.12.8'