[Debian-med-packaging] Bug#733352: Help with C++ issue: tophat does not build from source

[Andreas Tille]

Hi,

since the Build-Depends seqan-dev was upgraded from version 1.3 to 1.4
tophat fails to build from source (#733352).  I upgraded the Git repository
to the latest upstream version (2.0.11+dfsg) which unfortunately does not
help in this respect.

  Vcs-Git: git://anonscm.debian.org/debian-med/tophat.git

I wonder, whether some skilled C++ coder might be able to help with this
probably simple problem:


fiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(const THost_&, typename seqan::EnableIf<seqan::IsSameType<THost, THost_> >::Type*) [with THost_ = seqan::String<seqan::SimpleType<unsigned char,     seqan::Dna_>, seqan::Alloc<> >; THost = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >; TFunctor = seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna_> >;       typename seqan::EnableIf<seqan::IsSameType<THost, THost_> >::Type = void]':
/usr/include/seqan/modifier/modifier_reverse.h:153:33:   required from 'seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >::ModifiedString(const THost_&, typename seqan::EnableIf<seqan::And<seqan::  Not<seqan::IsSameType<typename seqan::InnermostHost_<seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> > >::Type, THost> >, seqan::IsSameType<typename seqan::InnermostHost_<seqan::                    ModifiedString<THost, seqan::Tag<seqan::ModReverse_> > >::Type, THost_> > >::Type*) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >; THost = seqan::                 ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna_> > > >; typename seqan::       EnableIf<seqan::And<seqan::Not<seqan::IsSameType<typename seqan::InnermostHost_<seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> > >::Type, THost> >, seqan::IsSameType<typename seqan::               InnermostHost_<seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> > >::Type, THost_> > >::Type = void]'
segment_juncs.cpp:2059:66:   required from 'void juncs_from_ref_segs(RefSequenceTable&, std::vector<RefSeg>&, PotentialJuncs&, const DnaString&, const DnaString&, int, int, size_t, bool, size_t) [with          JunctionRecorder = RecordSegmentJuncs; PotentialJuncs = std::set<Junction, skip_count_lt>; seqan::DnaString = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >; size_t = long        unsigned int]'
segment_juncs.cpp:3723:12:   required from here
/usr/include/seqan/modifier/modifier_view.h:151:34: error: invalid conversion from 'seqan::Pointer_<const seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> > >::Type {aka const seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >*}' to 'seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >, seqan::ModView<seqan::         FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna_> > > >::THostPointer_ {aka seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >*}' [-fpermissive]
             _host(_toPointer(host)), _cargo(), tmp_value()
                                  ^
make[3]: *** [segment_juncs.o] Error 1

Kind regards

    Andreas.


-- 
http://fam-tille.de