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.gruening@gmail.com>
Sent: Wednesday 15th June 2016 9:09
To: Peter van Heusden <pvh@sanbi.ac.za>; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Infinite recursion on conda dependency managerHi 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
>
>
>
> ___________________________________________________________
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___________________________________________________________
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