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

Charles Plessy plessy at debian.org
Wed Apr 4 04:03:40 UTC 2012 

Dear Ben and Cole,

Debian distributes bowtie, and after a mass-rebuild against GCC 4.7, we
noticed the following error:

  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]

You can see below for more context, and more in particular the instructions
under “Name lookup changes” in GCC's 4.7 porting page.

  http://gcc.gnu.org/gcc-4.7/porting_to.html

Do you think you can release an updated version of bowtie ?

I am sending a copy of this message in our public bug tracker
(667120 at bugs.debian.org).  Please feel free to do the same in your answer. 
The archive is available at the following URL.

  http://bugs.debian.org/667120

Have a nice day,

-- Charles Plessy, Debian Med packaging team, Tsurumi, Kanagawa, Japan.

Le Tue, Apr 03, 2012 at 11:08:03PM +0000, Matthias Klose a écrit :
> 
> 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
> 
> 
> 

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-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

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