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  1. BioC_mirror: http://bioconductor.org
  2. Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version
  3. 3.1.0.
  4. Installing package(s) 'Rbowtie'
  5. essai de l'URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Rbowtie_1.4.4.tar.gz'
  6. Content type 'application/x-gzip' length 880659 bytes (860 Kb)
  7. URL ouverte
  8. ==================================================
  9. downloaded 860 Kb
  10.  
  11. * installing *source* package ‘Rbowtie’ ...
  12. ** libs
  13. ** arch -
  14. g++ -O3 -m32 -DCOMPILER_OPTIONS="\"-O3 -m32 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g \
  15. -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
  16. -I SeqAn-1.1 -I third_party \
  17. -o bowtie-build ebwt_build.cpp \
  18. ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp bowtie_build_main.cpp \
  19. -lpthread
  20. In file included from SeqAn-1.1/seqan/basic.h:64:0,
  21. from SeqAn-1.1/seqan/sequence.h:27,
  22. from SeqAn-1.1/seqan/index.h:27,
  23. from ebwt_build.cpp:5:
  24. SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)’:
  25. SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  26. typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
  27. ^
  28. 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>&)’:
  29. SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  30. typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
  31. ^
  32. SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’:
  33. SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs]
  34. typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
  35. ^
  36. In file included from SeqAn-1.1/seqan/sequence.h:38:0,
  37. from SeqAn-1.1/seqan/index.h:27,
  38. from ebwt_build.cpp:5:
  39. SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)’:
  40. SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs]
  41. typedef typename Value<TLeft>::Type TLeftValue;
  42. ^
  43. In file included from SeqAn-1.1/seqan/sequence.h:51:0,
  44. from SeqAn-1.1/seqan/index.h:27,
  45. from ebwt_build.cpp:5:
  46. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
  47. SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  48. typedef String<TTargetValue, TTargetSpec> TTarget;
  49. ^
  50. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’:
  51. SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  52. typedef String<TTargetValue, TTargetSpec> TTarget;
  53. ^
  54. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’:
  55. SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  56. typedef String<TTargetValue, TTargetSpec> TTarget;
  57. ^
  58. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’:
  59. SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  60. typedef String<TTargetValue, TTargetSpec> TTarget;
  61. ^
  62. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
  63. SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  64. typedef String<TTargetValue, TTargetSpec> TTarget;
  65. ^
  66. 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>)’:
  67. SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  68. typedef String<TTargetValue, TTargetSpec> TTarget;
  69. ^
  70. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’:
  71. SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  72. typedef String<TTargetValue, TTargetSpec> TTarget;
  73. ^
  74. 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>)’:
  75. SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  76. typedef String<TTargetValue, TTargetSpec> TTarget;
  77. ^
  78. 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>)’:
  79. SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  80. typedef String<TTargetValue, TTargetSpec> TTarget;
  81. ^
  82. 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>)’:
  83. SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  84. typedef String<TTargetValue, TTargetSpec> TTarget;
  85. ^
  86. 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>)’:
  87. SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  88. typedef String<TTargetValue, TTargetSpec> TTarget;
  89. ^
  90. 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>)’:
  91. SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  92. typedef String<TTargetValue, TTargetSpec> TTarget;
  93. ^
  94. In file included from SeqAn-1.1/seqan/sequence.h:53:0,
  95. from SeqAn-1.1/seqan/index.h:27,
  96. from ebwt_build.cpp:5:
  97. 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)’:
  98. SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  99. typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
  100. ^
  101. In file included from SeqAn-1.1/seqan/sequence.h:57:0,
  102. from SeqAn-1.1/seqan/index.h:27,
  103. from ebwt_build.cpp:5:
  104. 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)’:
  105. SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs]
  106. typedef typename Iterator<T, Standard>::Type TIterator;
  107. ^
  108. 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)’:
  109. SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  110. typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
  111. ^
  112. In file included from SeqAn-1.1/seqan/sequence.h:62:0,
  113. from SeqAn-1.1/seqan/index.h:27,
  114. from ebwt_build.cpp:5:
  115. 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)’:
  116. SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs]
  117. typedef typename Id<TStringSet>::Type TId;
  118. ^
  119. In file included from SeqAn-1.1/seqan/index.h:82:0,
  120. from ebwt_build.cpp:5:
  121. 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)’:
  122. SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
  123. typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
  124. ^
  125. 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)’:
  126. SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
  127. typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
  128. ^
  129. SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  130. typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
  131. ^
  132. 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)’:
  133. SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
  134. typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
  135. ^
  136. 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)’:
  137. SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
  138. typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
  139. ^
  140. 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)’:
  141. SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
  142. typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
  143. ^
  144. In file included from SeqAn-1.1/seqan/index.h:83:0,
  145. from ebwt_build.cpp:5:
  146. 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)’:
  147. SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
  148. typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
  149. ^
  150. 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)’:
  151. SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
  152. typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
  153. ^
  154. 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)’:
  155. SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs]
  156. typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
  157. ^
  158. In file included from SeqAn-1.1/seqan/file.h:66:0,
  159. from ebwt_build.cpp:7:
  160. SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’:
  161. SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
  162. typedef typename Row<TAlign>::Type TRow;
  163. ^
  164. SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)’:
  165. SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs]
  166. typedef typename Position<TAlign>::Type TPosition;
  167. ^
  168. In file included from SeqAn-1.1/seqan/file.h:69:0,
  169. from ebwt_build.cpp:7:
  170. SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)’:
  171. SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
  172. typedef typename Row<TAlign>::Type TRow;
  173. ^
  174. In file included from ebwt.h:27:0,
  175. from ebwt_build.cpp:11:
  176. blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::buildSamples()’:
  177. blockwise_sa.h:380:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs]
  178. typedef typename Value<TStr>::Type TAlphabet;
  179. ^
  180. blockwise_sa.h: In member function ‘virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()’:
  181. blockwise_sa.h:745:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs]
  182. typedef typename Value<TStr>::Type TAlphabet;
  183. ^
  184. In file included from SeqAn-1.1/seqan/sequence.h:57:0,
  185. from SeqAn-1.1/seqan/index.h:27,
  186. from ebwt_build.cpp:5:
  187. 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<> > >’:
  188. 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 = unsigned int]’
  189. 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 = int]’
  190. 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 = unsigned int]’
  191. blockwise_sa.h:354:42: required from here
  192. 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]
  193. VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
  194. ^
  195. SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of ‘struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >’:
  196. 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 = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type = unsigned int]’
  197. ebwt.h:4022:32: 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]’
  198. ebwt_build.cpp:458:9: 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>]’
  199. ebwt_build.cpp:595:69: required from here
  200. 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]
  201. ebwt.h: Assembler messages:
  202. ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
  203. ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
  204. ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
  205. ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
  206. In file included from SeqAn-1.1/seqan/basic.h:64:0,
  207. from SeqAn-1.1/seqan/sequence.h:27,
  208. from ref_read.h:11,
  209. from ref_read.cpp:1:
  210. SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)’:
  211. SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  212. typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
  213. ^
  214. 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>&)’:
  215. SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  216. typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
  217. ^
  218. SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’:
  219. SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs]
  220. typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
  221. ^
  222. In file included from SeqAn-1.1/seqan/sequence.h:38:0,
  223. from ref_read.h:11,
  224. from ref_read.cpp:1:
  225. SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)’:
  226. SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs]
  227. typedef typename Value<TLeft>::Type TLeftValue;
  228. ^
  229. In file included from SeqAn-1.1/seqan/sequence.h:51:0,
  230. from ref_read.h:11,
  231. from ref_read.cpp:1:
  232. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
  233. SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  234. typedef String<TTargetValue, TTargetSpec> TTarget;
  235. ^
  236. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’:
  237. SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  238. typedef String<TTargetValue, TTargetSpec> TTarget;
  239. ^
  240. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’:
  241. SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  242. typedef String<TTargetValue, TTargetSpec> TTarget;
  243. ^
  244. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’:
  245. SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  246. typedef String<TTargetValue, TTargetSpec> TTarget;
  247. ^
  248. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
  249. SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  250. typedef String<TTargetValue, TTargetSpec> TTarget;
  251. ^
  252. 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>)’:
  253. SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  254. typedef String<TTargetValue, TTargetSpec> TTarget;
  255. ^
  256. SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’:
  257. SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  258. typedef String<TTargetValue, TTargetSpec> TTarget;
  259. ^
  260. 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>)’:
  261. SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  262. typedef String<TTargetValue, TTargetSpec> TTarget;
  263. ^
  264. 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>)’:
  265. SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  266. typedef String<TTargetValue, TTargetSpec> TTarget;
  267. ^
  268. 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>)’:
  269. SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  270. typedef String<TTargetValue, TTargetSpec> TTarget;
  271. ^
  272. 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>)’:
  273. SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  274. typedef String<TTargetValue, TTargetSpec> TTarget;
  275. ^
  276. 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>)’:
  277. SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  278. typedef String<TTargetValue, TTargetSpec> TTarget;
  279. ^
  280. In file included from SeqAn-1.1/seqan/sequence.h:53:0,
  281. from ref_read.h:11,
  282. from ref_read.cpp:1:
  283. 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)’:
  284. SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  285. typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
  286. ^
  287. In file included from SeqAn-1.1/seqan/sequence.h:57:0,
  288. from ref_read.h:11,
  289. from ref_read.cpp:1:
  290. 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)’:
  291. SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs]
  292. typedef typename Iterator<T, Standard>::Type TIterator;
  293. ^
  294. 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)’:
  295. SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  296. typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
  297. ^
  298. In file included from SeqAn-1.1/seqan/sequence.h:62:0,
  299. from ref_read.h:11,
  300. from ref_read.cpp:1:
  301. 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)’:
  302. SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs]
  303. typedef typename Id<TStringSet>::Type TId;
  304. ^
  305. In file included from SeqAn-1.1/seqan/file.h:66:0,
  306. from alphabet.h:7,
  307. from ref_read.h:12,
  308. from ref_read.cpp:1:
  309. SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)’:
  310. SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
  311. typedef typename Row<TAlign>::Type TRow;
  312. ^
  313. SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)’:
  314. SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs]
  315. typedef typename Position<TAlign>::Type TPosition;
  316. ^
  317. In file included from SeqAn-1.1/seqan/file.h:69:0,
  318. from alphabet.h:7,
  319. from ref_read.h:12,
  320. from ref_read.cpp:1:
  321. SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)’:
  322. SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
  323. typedef typename Row<TAlign>::Type TRow;
  324. ^
  325. make: *** [bowtie-build] Erreur 1
  326. ERROR: compilation failed for package ‘Rbowtie’
  327. * removing ‘/home/retureau/R/i686-pc-linux-gnu-library/3.1/Rbowtie’
  328.  
  329. The downloaded source packages are in
  330. ‘/tmp/Rtmp9xIsEn/downloaded_packages’
  331. Message d'avis :
  332. In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  333. installation of package ‘Rbowtie’ had non-zero exit status
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