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.
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