Your message dated Sun, 22 Apr 2012 16:32:12 +0000
with message-id <[email protected]>
and subject line Bug#667134: fixed in cd-hit 4.5.8-2012-03-24-1
has caused the Debian Bug report #667134,
regarding cd-hit: 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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--
667134: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=667134
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: cd-hit
Version: 4.5.7-1
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.
cdhit-common.h:95:4: error: 'push_back' 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/cd-hit_4.5.7-1_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.
[...]
dh_auto_configure -a
dh_auto_build -a
make[1]: Entering directory `/«PKGBUILDDIR»'
g++ -DNO_OPENMP -O2 cdhit-common.c++ -c
In file included from cdhit-common.c++:28:0:
cdhit-common.h: In instantiation of 'void Vector<TYPE>::Append(const TYPE&)
[with TYPE = NVector<long int>]':
cdhit-common.c++:716:27: required from here
cdhit-common.h:95:4: error: 'push_back' was not declared in this scope, and no
declarations were found by argument-dependent lookup at the point of
instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base
'std::vector<NVector<long int>, std::allocator<NVector<long int> > >' are not
found by unqualified lookup
cdhit-common.h:95:4: note: use 'this->push_back' instead
cdhit-common.h: In instantiation of 'void Vector<TYPE>::Append(const TYPE&)
[with TYPE = NVector<int>]':
cdhit-common.c++:717:25: required from here
cdhit-common.h:95:4: error: 'push_back' was not declared in this scope, and no
declarations were found by argument-dependent lookup at the point of
instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base
'std::vector<NVector<int>, std::allocator<NVector<int> > >' are not found by
unqualified lookup
cdhit-common.h:95:4: note: use 'this->push_back' instead
cdhit-common.h: In instantiation of 'void Vector<TYPE>::Append(const TYPE&)
[with TYPE = Sequence*]':
cdhit-common.c++:1260:24: required from here
cdhit-common.h:95:4: error: 'push_back' was not declared in this scope, and no
declarations were found by argument-dependent lookup at the point of
instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base
'std::vector<Sequence*, std::allocator<Sequence*> >' are not found by
unqualified lookup
cdhit-common.h:95:4: note: use 'this->push_back' instead
cdhit-common.h: In instantiation of 'void Vector<TYPE>::Append(const TYPE&)
[with TYPE = int]':
cdhit-common.c++:1925:26: required from here
cdhit-common.h:95:4: error: 'push_back' was not declared in this scope, and no
declarations were found by argument-dependent lookup at the point of
instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base 'std::vector<int,
std::allocator<int> >' are not found by unqualified lookup
cdhit-common.h:95:4: note: use 'this->push_back' instead
make[1]: *** [cdhit-common.o] Error 1
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_build: make -j1 returned exit code 2
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--- End Message ---
--- Begin Message ---
Source: cd-hit
Source-Version: 4.5.8-2012-03-24-1
We believe that the bug you reported is fixed in the latest version of
cd-hit, which is due to be installed in the Debian FTP archive:
cd-hit_4.5.8-2012-03-24-1.debian.tar.gz
to main/c/cd-hit/cd-hit_4.5.8-2012-03-24-1.debian.tar.gz
cd-hit_4.5.8-2012-03-24-1.dsc
to main/c/cd-hit/cd-hit_4.5.8-2012-03-24-1.dsc
cd-hit_4.5.8-2012-03-24-1_amd64.deb
to main/c/cd-hit/cd-hit_4.5.8-2012-03-24-1_amd64.deb
cd-hit_4.5.8-2012-03-24.orig.tar.gz
to main/c/cd-hit/cd-hit_4.5.8-2012-03-24.orig.tar.gz
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 cd-hit 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 18:06:41 +0200
Source: cd-hit
Binary: cd-hit
Architecture: source amd64
Version: 4.5.8-2012-03-24-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
cd-hit - suite of programs designed to quickly group sequences
Closes: 667134
Changes:
cd-hit (4.5.8-2012-03-24-1) unstable; urgency=low
.
[ Charles Plessy ]
* renamed debian/upstream-metadata.yaml to debian/upstream
.
[ Andreas Tille ]
* New upstream version
* debian/watch: Fixed to reflect the change on code.google.com
* debian/control: Standards-Version: 3.9.3 (no changes needed)
* debian/copyright: Fixed DEP5 and verified using
cme fix dpkg-copyright
* debian/patches/gcc-4.7.patch: Enable building with g++-4.7
Closes: #667134
* debian/upstream:
- use BibTeX format to specify author
- Move DOI+PMID to References
- Differentiate between URl and eprint
* debhelper 9 (control+compat)
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