[Debian-med-packaging] Bug#733352: tophat: FTBFS: string_base.h:1465:53: error: no matching function for call to 'seqan::Gaps<seqan::String<char, seqan::Alloc<> >, seqan::Tag<seqan::ArrayGaps_> >::Gaps(const seqan::String<char, seqan::Alloc<> >&)'

[David Suárez]

Source: tophat
Version: 2.0.10-1
Severity: serious
Tags: jessie sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20131226 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully):
> g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include  -I./SeqAn-1.3 -c -o segment_juncs.o segment_juncs.cpp
> In file included from segment_juncs.cpp:37:0:
> common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
> common.h:578:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
>       int     pre_block_offs=0; //but before this write()
>               ^
> segment_juncs.cpp: In member function 'void SegmentSearchWorker::operator()()':
> segment_juncs.cpp:4720:27: warning: variable 'last_read_id' set but not used [-Wunused-but-set-variable]
>      uint64_t read_id = 0, last_read_id = 0;
>                            ^
> In file included from /usr/include/seqan/sequence.h:82:0,
>                  from segment_juncs.cpp:27:
> /usr/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_<TExpand>::appendValue_(T&, TValue&) [with T = seqan::String<seqan::Gaps<seqan::String<char, seqan::Alloc<> >, seqan::Tag<seqan::ArrayGaps_> >, seqan::Alloc<> >; TValue = const seqan::String<char, seqan::Alloc<> >; TExpand = seqan::Tag<seqan::TagGenerous_>]':
> /usr/include/seqan/sequence/string_base.h:1490:65:   required from 'void seqan::appendValue(seqan::String<TValue, TSpec>&, const TValue&, seqan::Tag<TUsage>) [with TTargetValue = seqan::Gaps<seqan::String<char, seqan::Alloc<> >, seqan::Tag<seqan::ArrayGaps_> >; TTargetSpec = seqan::Alloc<>; TValue = seqan::String<char, seqan::Alloc<> >; TExpand = seqan::TagGenerous_]'
> /usr/include/seqan/sequence/sequence_interface.h:1241:72:   required from 'void seqan::appendValue(T&, const TValue&) [with T = seqan::String<seqan::Gaps<seqan::String<char, seqan::Alloc<> >, seqan::Tag<seqan::ArrayGaps_> >, seqan::Alloc<> >; TValue = seqan::String<char, seqan::Alloc<> >]'
> segment_juncs.cpp:2605:32:   required from here
> /usr/include/seqan/sequence/string_base.h:1465:53: error: no matching function for call to 'seqan::Gaps<seqan::String<char, seqan::Alloc<> >, seqan::Tag<seqan::ArrayGaps_> >::Gaps(const seqan::String<char, seqan::Alloc<> >&)'
>              typename Value<T>::Type temp_copy(_value); //temp copy because resize could invalidate _value
>                                                      ^
> /usr/include/seqan/sequence/string_base.h:1465:53: note: candidates are:
> In file included from /usr/include/seqan/align.h:76:0,
>                  from segment_juncs.cpp:31:
> /usr/include/seqan/align/gaps_array.h:156:5: note: seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >::Gaps(const seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&) [with TSequence = seqan::String<char, seqan::Alloc<> >]
>      Gaps(Gaps const & other) :
>      ^
> /usr/include/seqan/align/gaps_array.h:156:5: note:   no known conversion for argument 1 from 'const seqan::String<char, seqan::Alloc<> >' to 'const seqan::Gaps<seqan::String<char, seqan::Alloc<> >, seqan::Tag<seqan::ArrayGaps_> >&'
> /usr/include/seqan/align/gaps_array.h:146:5: note: seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >::Gaps(TSequence&) [with TSequence = seqan::String<char, seqan::Alloc<> >]
>      Gaps(TSequence & seq) :
>      ^
> /usr/include/seqan/align/gaps_array.h:146:5: note:   no known conversion for argument 1 from 'const seqan::String<char, seqan::Alloc<> >' to 'seqan::String<char, seqan::Alloc<> >&'
> /usr/include/seqan/align/gaps_array.h:141:5: note: seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >::Gaps() [with TSequence = seqan::String<char, seqan::Alloc<> >]
>      Gaps() : _sourceBeginPos(0), _sourceEndPos(0), _clippingBeginPos(0), _clippingEndPos(0)//,
>      ^
> /usr/include/seqan/align/gaps_array.h:141:5: note:   candidate expects 0 arguments, 1 provided
> In file included from /usr/include/seqan/modifier.h:67:0,
>                  from /usr/include/seqan/find.h:44,
>                  from segment_juncs.cpp:28:
> /usr/include/seqan/modifier/modifier_view.h: In instantiation of 'seqan::ModifiedString<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

The full build log is available from:
   http://aws-logs.debian.net/ftbfs-logs/2013/12/26/tophat_2.0.10-1_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.