Hi Philipp, you are inside of the Docker container?
Can you do a: export PATH=/galaxy-central/tool_deps/_conda/bin/:$PATH conda install -y -q conda=3.19.3 Ciao, Bjoern Am 20.06.2016 um 13:01 schrieb Rathert, Philipp, Dr.: > Dear all, > > > > > > I am trying to install bowtie as a dependency for bismarck. however, I am > getting the error posted below. > > > > Maybe somebody has an idea how to fix this. > > > > > > Thanks in advance, > > > > philipp > > > > > > 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] > typedef 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] > typedef 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] > > .. > 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 alphabet.h:6, > from color_dec.cpp:11: > 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 alphabet.h:6, > from color_dec.cpp:11: > 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 alphabet.h:6, > from color_dec.cpp:11: > 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 color_dec.cpp:11: > 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 color_dec.cpp:11: > 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; > ^ > 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&)’: > color_dec.cpp:187:6: warning: variable ‘lastOmin’ set but not used > [-Wunused-but-set-variable] > int lastOmin = INT_MAX; > ^ > In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from hit.h:11, > from hit.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 hit.h:11, > from hit.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 hit.h:11, > from hit.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 hit.h:11, > from hit.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 hit.h:11, > from hit.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 hit.h:11, > from hit.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 hit.h:12, > from hit.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 hit.h:12, > from hit.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; > ^ > make: *** [bowtie] Error 1 > > > > > > > > > > > > -----Original message----- > From: Björn Grüning <bjoern.gruen...@gmail.com> > Sent: Wednesday 15th June 2016 9:09 > To: Peter van Heusden <p...@sanbi.ac.za>; galaxy-dev@lists.galaxyproject.org > Subject: Re: [galaxy-dev] Infinite recursion on conda dependency manager > > > Hi Peter, > > please install conda in version 3.19.3. Conda-4 has a bug when using > with --offline and --local. > > conda install conda=3.19.3 should work. > > https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L15 > > Thanks, > Bjoern > > Am 15.06.2016 um 00:44 schrieb Peter van Heusden: >> Hi there >> >> I've got a package in our lab conda channel (its still in testing phase) >> called goget. This is specified as a requirement for the build_ctb_gene >> tool like this: >> >> <requirements> >> <requirement type="package" version="0.0.1">goget</requirement> >> </requirements> >> >> When the tool runs, I see infinite recursion on the conda side: >> >> https://gist.github.com/pvanheus/c16a07a2c954741a311881cc7606df8d >> >> Any ideas? >> >> Thanks, >> Peter >> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
