Hi, similarly to the plink case I can not found an easy solution for this problem.
Kind regards Andreas. ----- Forwarded message from Matthias Klose <d...@debian.org> ----- Date: Tue, 03 Apr 2012 23:08:03 +0000 From: Matthias Klose <d...@debian.org> To: mainto...@bugs.debian.org Subject: Bug#667120: bowtie: ftbfs with GCC-4.7 X-Debian-PR-Message: report 667120 X-Debian-PR-Package: bowtie X-Debian-PR-Keywords: sid wheezy X-Debian-PR-Source: bowtie Package: bowtie Version: 0.12.7-1 Severity: important Tags: sid wheezy User: debian-...@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 _______________________________________________ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging ----- End forwarded message ----- -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of "unsubscribe". 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