[Debian-med-packaging] Bug#667134: cd-hit: ftbfs with GCC-4.7

[Matthias Klose]

Package: cd-hit
Version: 4.5.7-1
Severity: important
Tags: sid wheezy
User: debian-gcc at 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.

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