Hi Cole,
when building the tophat Debian package we were using the Debian
packaged seqan library which worked as long as we had seqan 1.3.1.
Since the migration to seqan 1.4.1 this stoped working (see below). So
the question is: Do we find some patch to comply with seqan 1.4.x
(preferable), do we consider maintaining a versioned seqan1.3-dev
package inside Debian to cope with tophat and other packages with the
same problem (creates extra work) or do we go the wimpy trail and simply
revert to the seqan-1.1 convenience copy included inside the tophat
source?
Kind regards
Andreas.
----- Forwarded message from David Suárez <david.sephi...@gmail.com> -----
Date: Sat, 28 Dec 2013 20:02:15 +0100
From: David Suárez <david.sephi...@gmail.com>
To: sub...@bugs.debian.org
Subject: 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<> >&)'
X-Debian-PR-Message: report 733352
X-Debian-PR-Package: src:tophat
X-Debian-PR-Keywords: jessie sid
X-Debian-PR-Source: tophat
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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