Re: Help needed to fix g++ 4.7 error [Was: Bug#667120: bowtie: ftbfs with GCC-4.7]
On Sun, 22 Apr 2012, Andreas Tille escribió:
> Hi,
>
> similarly to the plink case I can not found an easy solution for this
> problem.
>
> Kind regards
I didn't have gcc 4.7, therefore I don't have the problem. IMO the problem is that the function "reverseInPlace" is declared after the function is used.
Is defined at line 74, but used at 48.
Probably the easiest solution is moving the block:
/// Reverse a string in-place
template <typename TStr>
static inline void reverseInPlace(TStr& s) {
typedef typename Value<TStr>::Type TVal;
size_t len = length(s);
for(size_t i = 0; i < (len>>1); i++) {
TVal tmp = s[i];
s[i] = s[len-i-1];
s[len-i-1] = tmp;
}
}
before the function reverseComplementInPlace or create a function prototype (before the line 48 too):
template <typename TStr>
static inline void reverseInPlace(TStr& s);
I hope this helps.
Saludos,
kix
> Andreas.
>
> ----- Forwarded message from Matthias Klose <doko@debian.org> -----
>
> Date: Tue, 03 Apr 2012 23:08:03 +0000
> From: Matthias Klose <doko@debian.org>
> To: maintonly@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-gcc@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
>
>
>
>
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--
||// //\\// Rodolfo "kix" Garcia
||\\// //\\ http://www.kix.es/
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