Re: [galaxy-dev] Infinite recursion on conda dependency manager

20 Jun 2016

      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 manager

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;
                                                           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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Rathert, Philipp, Dr.

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