Source: tophat
Version: 2.0.10-1
Severity: serious
Tags: jessie sid
User: debian...@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.
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