Your message dated Mon, 23 Apr 2012 10:47:14 +0000
with message-id <[email protected]>
and subject line Bug#667120: fixed in bowtie 0.12.7-2
has caused the Debian Bug report #667120,
regarding bowtie: ftbfs with GCC-4.7
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
667120: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=667120
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: bowtie
Version: 0.12.7-1
Severity: important
Tags: sid wheezy
User: [email protected]
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
--- End Message ---
--- Begin Message ---
Source: bowtie
Source-Version: 0.12.7-2
We believe that the bug you reported is fixed in the latest version of
bowtie, which is due to be installed in the Debian FTP archive:
bowtie-examples_0.12.7-2_all.deb
to main/b/bowtie/bowtie-examples_0.12.7-2_all.deb
bowtie_0.12.7-2.debian.tar.gz
to main/b/bowtie/bowtie_0.12.7-2.debian.tar.gz
bowtie_0.12.7-2.dsc
to main/b/bowtie/bowtie_0.12.7-2.dsc
bowtie_0.12.7-2_amd64.deb
to main/b/bowtie/bowtie_0.12.7-2_amd64.deb
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated bowtie package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Sun, 22 Apr 2012 21:09:05 +0200
Source: bowtie
Binary: bowtie bowtie-examples
Architecture: source amd64 all
Version: 0.12.7-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
bowtie - ultrafast memory-efficient short read aligner
bowtie-examples - Examples for bowtie, the ultrafast memory-efficient short
read al
Closes: 667120
Changes:
bowtie (0.12.7-2) unstable; urgency=low
.
* Do not give a pointer to non existing info pages in manpages
* debian/control:
- fixed Vcs fields
- Standards-Version: 3.9.3 (no changes needed)
* debian/upstream: Add citation information
* debian/rules: calculate pkg name instead of setting it
* debian/copyright: DEP5 verified using
cme fix dpkg-copyright
* debian/patches/gcc-4.7.patch: function "reverseInPlace" is declared after
the function is used
Thanks to Rodolfo García Peñas <[email protected]> and
gregor herrmann <[email protected]>
Closes: #667120
* debhelper 9 (control+compat)
Hardening flags were explicitly tested but not enforced in debian/rules
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--- End Message ---
