1. * Package: sci-biology/bowtie-0.12.7
  2. * Repository: gentoo
  3. * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
  4. * USE: amd64 elibc_glibc kernel_linux multilib test userland_GNU
  5. * FEATURES: sandbox test userpriv usersandbox
  6. >>> Unpacking source...
  7. >>> Unpacking bowtie-0.12.7-src.zip to /tmp/portage/sci-biology/bowtie-0.12.7/work
  8. >>> Source unpacked in /tmp/portage/sci-biology/bowtie-0.12.7/work
  9. >>> Preparing source in /tmp/portage/sci-biology/bowtie-0.12.7/work/bowtie-0.12.7 ...
  10. >>> Source prepared.
  11. >>> Configuring source in /tmp/portage/sci-biology/bowtie-0.12.7/work/bowtie-0.12.7 ...
  12. >>> Source configured.
  13. >>> Compiling source in /tmp/portage/sci-biology/bowtie-0.12.7/work/bowtie-0.12.7 ...
  14. make -j24 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=
  15. cat ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp pool.h filebuf.h bitset.h log.h auto_array.h assert_helpers.h range_cache.h range_chaser.h ebwt.h row_chaser.h hit.h range.h endian_swap.h mm.h hit_set.h binary_sa_search.h pat.h color_dec.h refmap.h ebwt_search_util.h aligner.h sam.h random_source.h reference.h multikey_qsort.h word_io.h sequence_io.h ref_aligner.h diff_sample.h annot.h aligner_seed_mm.h blockwise_sa.h alphabet.h range_source.h search_globals.h spinlock.h ref_read.h zbox.h aligner_23mm.h color.h threading.h timer.h str_util.h bitpack.h shmem.h aligner_0mm.h formats.h ebwt_search_backtrack.h tokenize.h qual.h edit.h aligner_1mm.h aligner_metrics.h | md5sum | awk '{print $1}' > .bowtie-build.md5
  16. 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 bitset.h log.h auto_array.h assert_helpers.h range_cache.h range_chaser.h ebwt.h row_chaser.h hit.h range.h endian_swap.h mm.h hit_set.h binary_sa_search.h pat.h color_dec.h refmap.h ebwt_search_util.h aligner.h sam.h random_source.h reference.h multikey_qsort.h word_io.h sequence_io.h ref_aligner.h diff_sample.h annot.h aligner_seed_mm.h blockwise_sa.h alphabet.h range_source.h search_globals.h spinlock.h ref_read.h zbox.h aligner_23mm.h color.h threading.h timer.h str_util.h bitpack.h shmem.h aligner_0mm.h formats.h ebwt_search_backtrack.h tokenize.h qual.h edit.h aligner_1mm.h aligner_metrics.h search_seeded_phase3.c search_23mm_phase3.c search_seeded_phase2.c search_23mm_phase2.c search_23mm_phase1.c search_1mm_phase1.c search_1mm_phase2.c search_seeded_phase4.c search_seeded_phase1.c | md5sum | awk '{print $1}' > .bowtie.md5
  17. cat bowtie_inspect.cpp pool.h filebuf.h bitset.h log.h auto_array.h assert_helpers.h range_cache.h range_chaser.h ebwt.h row_chaser.h hit.h range.h endian_swap.h mm.h hit_set.h binary_sa_search.h pat.h color_dec.h refmap.h ebwt_search_util.h aligner.h sam.h random_source.h reference.h multikey_qsort.h word_io.h sequence_io.h ref_aligner.h diff_sample.h annot.h aligner_seed_mm.h blockwise_sa.h alphabet.h range_source.h search_globals.h spinlock.h ref_read.h zbox.h aligner_23mm.h color.h threading.h timer.h str_util.h bitpack.h shmem.h aligner_0mm.h formats.h ebwt_search_backtrack.h tokenize.h qual.h edit.h aligner_1mm.h aligner_metrics.h ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp | md5sum | awk '{print $1}' > .bowtie-inspect.md5
  18. x86_64-pc-linux-gnu-g++ -DCOMPILER_OPTIONS="\" -Wl,-O1 -Wl,--as-needed -O2 -pipe -ggdb -march=native -ftracer \"" -Wl,-O1 -Wl,--as-needed -O2 -pipe -ggdb -march=native -ftracer \
  19. -DEBWT_BUILD_HASH=`cat .bowtie-build.md5` \
  20. -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 \
  21. -I SeqAn-1.1 \
  22. -o bowtie-build ebwt_build.cpp \
  23. ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp bowtie_build_main.cpp \
  24. x86_64-pc-linux-gnu-g++ \
  25. -DCOMPILER_OPTIONS="\" -Wl,-O1 -Wl,--as-needed -O2 -pipe -ggdb -march=native -ftracer \"" -Wl,-O1 -Wl,--as-needed -O2 -pipe -ggdb -march=native -ftracer \
  26. -DEBWT_INSPECT_HASH=`cat .bowtie-inspect.md5` \
  27. -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 -Wall \
  28. -I SeqAn-1.1 -I . \
  29. -o bowtie-inspect bowtie_inspect.cpp \
  30. ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp \
  31. x86_64-pc-linux-gnu-g++ -DCOMPILER_OPTIONS="\" -Wl,-O1 -Wl,--as-needed -O2 -pipe -ggdb -march=native -ftracer \"" -Wl,-O1 -Wl,--as-needed -O2 -pipe -ggdb -march=native -ftracer \
  32. -DEBWT_SEARCH_HASH=`cat .bowtie.md5` \
  33. -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 \
  34. -I SeqAn-1.1 \
  35. -o bowtie ebwt_search.cpp \
  36. 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 \
  37. -lpthread
  38. In file included from ebwt.h:1603:0,
  39. from ebwt_build.cpp:11:
  40. 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)':
  41. ebwt_search_backtrack.h:770:11: warning: variable 'foundTarget' set but not used [-Wunused-but-set-variable]
  42. In file included from ebwt.h:1603:0,
  43. from ebwt_search.cpp:15:
  44. 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)':
  45. ebwt_search_backtrack.h:770:11: warning: variable 'foundTarget' set but not used [-Wunused-but-set-variable]
  46. In file included from ebwt.h:24:0,
  47. from ebwt_build.cpp:11:
  48. alphabet.h: In instantiation of 'void reverseComplementInPlace(TStr&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >]':
  49. hit.h:97:45: required from here
  50. alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
  51. alphabet.h:74:20: note: 'template<class TStr> void reverseInPlace(TStr&)' declared here, later in the translation unit
  52. In file included from SeqAn-1.1/seqan/sequence.h:57:0,
  53. from SeqAn-1.1/seqan/index.h:27,
  54. from ebwt_build.cpp:5:
  55. 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<> > >':
  56. SeqAn-1.1/seqan/sequence/string_packed.h:906:131: 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]'
  57. 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]'
  58. SeqAn-1.1/seqan/sequence/string_base.h:181:51: 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]'
  59. blockwise_sa.h:354:32: required from here
  60. SeqAn-1.1/seqan/sequence/string_packed.h:291:2: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
  61. In file included from ebwt_search.cpp:1895:0:
  62. search_23mm_phase3.c: In function 'void* twoOrThreeMismatchSearchWorkerFull(void*)':
  63. search_23mm_phase3.c:27:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
  64. search_23mm_phase3.c:48:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
  65. In file included from ebwt_search.cpp:2164:0:
  66. search_seeded_phase3.c: In function 'void* seededQualSearchWorkerFull(void*)':
  67. search_seeded_phase3.c:64:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
  68. In file included from ebwt_search.cpp:2165:0:
  69. search_seeded_phase4.c:66:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
  70. In file included from ebwt_search.cpp:12:0:
  71. alphabet.h: In instantiation of 'void reverseComplementInPlace(TStr&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >]':
  72. hit.h:97:45: required from here
  73. alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
  74. alphabet.h:74:20: note: 'template<class TStr> void reverseInPlace(TStr&)' declared here, later in the translation unit
  75. SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
  76. SeqAn-1.1/seqan/sequence/string_packed.h:731:94: 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]'
  77. ebwt.h:3891:2: 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]'
  78. 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>]'
  79. ebwt_build.cpp:600:69: required from here
  80. SeqAn-1.1/seqan/sequence/string_packed.h:291:2: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
  81. In file included from SeqAn-1.1/seqan/sequence.h:57:0,
  82. from SeqAn-1.1/seqan/find.h:31,
  83. from ebwt_search.cpp:8:
  84. 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<> > >':
  85. SeqAn-1.1/seqan/sequence/string_packed.h:906:131: 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]'
  86. 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]'
  87. SeqAn-1.1/seqan/sequence/string_base.h:181:51: 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]'
  88. blockwise_sa.h:354:32: required from here
  89. SeqAn-1.1/seqan/sequence/string_packed.h:291:2: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
  90. In file included from ebwt.h:24:0,
  91. from bowtie_inspect.cpp:10:
  92. alphabet.h: In instantiation of 'void reverseComplementInPlace(TStr&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >]':
  93. hit.h:97:45: required from here
  94. alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
  95. alphabet.h:74:20: note: 'template<class TStr> void reverseInPlace(TStr&)' declared here, later in the translation unit
  96. ref_read.cpp: In function 'void reverseRefRecords(const std::vector<RefRecord>&, std::vector<RefRecord>&, bool, bool)':
  97. ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
  98. 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&)':
  99. ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
  100. ref_read.cpp: In function 'void reverseRefRecords(const std::vector<RefRecord>&, std::vector<RefRecord>&, bool, bool)':
  101. ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
  102. 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&)':
  103. ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
  104. In file included from SeqAn-1.1/seqan/sequence.h:57:0,
  105. from SeqAn-1.1/seqan/find.h:31,
  106. from bowtie_inspect.cpp:6:
  107. 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<> > >':
  108. SeqAn-1.1/seqan/sequence/string_packed.h:906:131: 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]'
  109. 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]'
  110. SeqAn-1.1/seqan/sequence/string_base.h:181:51: 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]'
  111. blockwise_sa.h:354:32: required from here
  112. SeqAn-1.1/seqan/sequence/string_packed.h:291:2: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
  113. SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
  114. SeqAn-1.1/seqan/sequence/string_packed.h:509:2: required from 'typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::capacity(const seqan::String<TValue, seqan::Packed<THostspec> >&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; THostspec = seqan::Alloc<void>; typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
  115. SeqAn-1.1/seqan/sequence/string_base.h:1429:52: required from 'static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TExpand = const seqan::Tag<seqan::TagExact_>; typename seqan::Size<T>::Type = long unsigned int]'
  116. SeqAn-1.1/seqan/sequence/string_base.h:1459:67: required from 'typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::resize(seqan::String<TValue, TSpec>&, TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]'
  117. ebwt.h:2807:2: required from 'void Ebwt<TStr>::restore(TStr&) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]'
  118. bowtie_inspect.cpp:267:2: required from 'void print_index_sequences(std::ostream&, Ebwt<TStr>&, const BitPairReference&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::ostream = std::basic_ostream<char>]'
  119. bowtie_inspect.cpp:445:42: required from here
  120. SeqAn-1.1/seqan/sequence/string_packed.h:291:2: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
  121. make: *** [bowtie-build] Error 1
  122. make: *** Waiting for unfinished jobs....
  123. ref_read.cpp: In function 'void reverseRefRecords(const std::vector<RefRecord>&, std::vector<RefRecord>&, bool, bool)':
  124. ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
  125. 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&)':
  126. ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
  127. make: *** [bowtie-inspect] Error 1
  128. In file included from hit.h:12:0,
  129. from ebwt_search_util.h:9,
  130. from ebwt_search_util.cpp:1:
  131. alphabet.h: In instantiation of 'void reverseComplementInPlace(TStr&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >]':
  132. hit.h:97:45: required from here
  133. alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
  134. alphabet.h:74:20: note: 'template<class TStr> void reverseInPlace(TStr&)' declared here, later in the translation unit
  135. In file included from hit_set.cpp:11:0:
  136. alphabet.h: In instantiation of 'void reverseComplementInPlace(TStr&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >]':
  137. hit_set.cpp:29:41: required from here
  138. alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
  139. alphabet.h:74:20: note: 'template<class TStr> void reverseInPlace(TStr&)' declared here, later in the translation unit
  140. sam.cpp: In static member function 'static void SAMHitSink::appendAligned(std::ostream&, const Hit&, int, int, const std::vector<std::basic_string<char> >*, ReferenceMap*, AnnotationMap*, bool, int)':
  141. sam.cpp:150:22: warning: variable 'pat' set but not used [-Wunused-but-set-variable]
  142. In file included from pat.h:13:0,
  143. from sam.cpp:11:
  144. alphabet.h: In instantiation of 'void reverseComplementInPlace(TStr&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >]':
  145. hit.h:97:45: required from here
  146. alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
  147. alphabet.h:74:20: note: 'template<class TStr> void reverseInPlace(TStr&)' declared here, later in the translation unit
  148. color_dec.cpp: In function 'void decodeHit(const char*, const char*, size_t, size_t, const char*, size_t, size_t, int, char*, char*, char*, int&, int&)':
  149. color_dec.cpp:187:6: warning: variable 'lastOmin' set but not used [-Wunused-but-set-variable]
  150. In file included from hit.h:12:0,
  151. from hit.cpp:1:
  152. alphabet.h: In instantiation of 'void reverseComplementInPlace(TStr&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >]':
  153. hit.h:97:45: required from here
  154. alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
  155. alphabet.h:74:20: note: 'template<class TStr> void reverseInPlace(TStr&)' declared here, later in the translation unit
  156. make: *** [bowtie] Error 1
  157. * ERROR: sci-biology/bowtie-0.12.7 failed (compile phase):
  158. * emake failed
  159. *
  160. * If you need support, post the output of `emerge --info '=sci-biology/bowtie-0.12.7'`,
  161. * the complete build log and the output of `emerge -pqv '=sci-biology/bowtie-0.12.7'`.
  162. * The complete build log is located at '/var/log/portage/sci-biology:bowtie-0.12.7:20120619-044616.log'.
  163. * For convenience, a symlink to the build log is located at '/tmp/portage/sci-biology/bowtie-0.12.7/temp/build.log'.
  164. * The ebuild environment file is located at '/tmp/portage/sci-biology/bowtie-0.12.7/temp/environment'.
  165. * Working directory: '/tmp/portage/sci-biology/bowtie-0.12.7/work/bowtie-0.12.7'
  166. * S: '/tmp/portage/sci-biology/bowtie-0.12.7/work/bowtie-0.12.7'
  167. nc6: using stream socket