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 (667...@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 > > > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". 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