[Debian-med-packaging] Bug#667120: bowtie: ftbfs with GCC-4.7

[Matthias Klose]

Package: bowtie
Version: 0.12.7-1
Severity: important
Tags: sid wheezy
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-4.7

The package fails to build in a test rebuild on at least amd64 with
gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The
severity of this report may be raised before the wheezy release.

alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]

The full build log can be found at:
http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/bowtie_0.12.7-1_unstable-gcc47.log
The last lines of the build log are at the end of this report.

Some hints on fixing these issues can be found at
http://gcc.gnu.org/gcc-4.7/porting_to.html

To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

[...]
In file included from ebwt.h:24:0,
                 from ebwt_build.cpp:11:
alphabet.h: In instantiation of 'void reverseComplementInPlace(TStr&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >]':
hit.h:97:45:   required from here
alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
alphabet.h:74:20: note: 'template<class TStr> void reverseInPlace(TStr&)' declared here, later in the translation unit
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:906:131:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_packed.h:1237:40:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
SeqAn-1.1/seqan/sequence/string_base.h:181:51:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
blockwise_sa.h:354:32:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:291:2: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:731:94:   required from 'typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Alloc<void>; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
ebwt.h:3891:2:   required from 'static TStr Ebwt<TStr>::join(std::vector<FileBuf*>&, std::vector<RefRecord>&, uint32_t, const RefReadInParams&, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; uint32_t = unsigned int]'
ebwt_build.cpp:463:9:   required from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::string = std::basic_string<char>]'
ebwt_build.cpp:600:69:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:291:2: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
ref_read.cpp: In function 'void reverseRefRecords(const std::vector<RefRecord>&, std::vector<RefRecord>&, bool, bool)':
ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'std::pair<long unsigned int, long unsigned int> fastaRefReadSizes(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, const RefReadInParams&, BitpairOutFileBuf*, int&)':
ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
make[2]: *** [bowtie-build] Error 1
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: *** [override_dh_auto_build] Error 2
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2