Hi Björn,
this is not working
root@galaxy:/galaxy-central# export PATH=/galaxy-central/tool_deps/_conda/bin/:$PATH
root@galaxy:/galaxy-central# conda install -y -q conda=3.19.3
bash: conda: command not found
cheers,
Philipp
-----Original message-----
From: Björn Grüning <bjoern.gruening@gmail.com>
Sent: Monday 20th June 2016 13:21
To: Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de>; galaxy-dev@lists.galaxyproject.org
Cc: Björn Grüning <bjoern.gruening@gmail.com>
Subject: Re: [galaxy-dev] Infinite recursion on conda dependency managerHi Philipp,
you are inside of the Docker container?
Can you do a:
export PATH=/galaxy-central/tool_deps/_conda/bin/:$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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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;
> ˆ
> 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 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
>>
>>
>>
>> ___________________________________________________________
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>>
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>>
> ___________________________________________________________
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>