[Debian-med-packaging] Bug#777922: jellyfish: ftbfs with GCC-5

[Andreas Tille]

Hi Guillaume,

there is a bug report against Jellyfish in Debian when trying to build
with gcc-5.  Since gcc-5 will be the default compiler in the next Debian
release this problem is critical.

If you have no idea how to fix this issue I would ask some c++ experts.

Kind regards and thanks for providing jellyfish as free software

      Andreas.

On Thu, Feb 12, 2015 at 10:32:46AM +0000, Matthias Klose wrote:
> Package: src:jellyfish
> Version: 2.1.4-1
> Severity: normal
> Tags: sid stretch
> User: debian-gcc at lists.debian.org
> Usertags: ftbfs-gcc-5
> 
> Please keep this issue open in the bug tracker for the package it
> was filed for.  If a fix in another package is required, please
> file a bug for the other package (or clone), and add a block in this
> package. Please keep the issue open until the package can be built in
> a follow-up test rebuild.
> 
> The package fails to build in a test rebuild on at least amd64 with
> gcc-5/g++-5, but succeeds to build with gcc-4.9/g++-4.9. The
> severity of this report may be raised before the stretch release.
> 
> The full build log can be found at:
> http://people.debian.org/~doko/logs/gcc5-20150205/jellyfish_2.1.4-1_unstable_gcc5.log
> The last lines of the build log are at the end of this report.
> 
> To build with GCC 5, either set CC=gcc-5 CXX=g++-5 explicitly,
> or install the gcc, g++, gfortran, ... packages from experimental.
> 
>   apt-get -t experimental install g++ 
> 
> Common build failures are C11 as the default C mode, new warnings
> resulting in build failures with -Werror turned on, or new/dropped
> symbols in Debian symbols files.  For other C/C++ related build failures
> see the porting guide at http://gcc.gnu.org/gcc-5/porting_to.html
> 
> [...]
> jellyfish/merge_files.cc:50:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
>  typedef std::auto_ptr<RectangularBinaryMatrix> matrix_ptr;
>               ^
> In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
>                  from /usr/include/c++/5/locale:43,
>                  from /usr/include/c++/5/iomanip:43,
>                  from ./include/jellyfish/err.hpp:21,
>                  from ./jellyfish/merge_files.hpp:21,
>                  from jellyfish/merge_files.cc:17:
> /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
>    template<typename> class auto_ptr;
>                             ^
>   CXXLD    bin/jellyfish
> make[3]: Leaving directory '/??PKGBUILDDIR??'
> make[2]: Leaving directory '/??PKGBUILDDIR??'
> make[1]: Leaving directory '/??PKGBUILDDIR??'
>    dh_auto_test -a
> make[1]: Entering directory '/??PKGBUILDDIR??'
> make  check-am
> make[2]: Entering directory '/??PKGBUILDDIR??'
> make  libgtest.la libgtest_main.la bin/generate_sequence bin/test_all
> make[3]: Entering directory '/??PKGBUILDDIR??'
>   CXX      unit_tests/gtest/src/libgtest_la-gtest-all.lo
>   CXXLD    libgtest.la
>   CXX      unit_tests/gtest/src/libgtest_main_la-gtest_main.lo
>   CXXLD    libgtest_main.la
>   CXX      jellyfish/generate_sequence.o
>   CXX      jellyfish/mersenne.o
>   CXX      jellyfish/backtrace.o
>   CXX      jellyfish/dbg.o
>   CXXLD    bin/generate_sequence
>   CXX      unit_tests/bin_test_all-test_main.o
> In file included from ./unit_tests/gtest/gtest.h:308:0,
>                  from unit_tests/test_main.cc:20:
> /usr/include/c++/5/sstream:335:7: error: 'struct std::basic_stringbuf<_CharT, _Traits, _Alloc>::__xfer_bufptrs' redeclared with different access
>        struct __xfer_bufptrs
>        ^
> make[3]: *** [unit_tests/bin_test_all-test_main.o] Error 1
> Makefile:1285: recipe for target 'unit_tests/bin_test_all-test_main.o' failed
> make[3]: Leaving directory '/??PKGBUILDDIR??'
> make[2]: *** [check-am] Error 2
> Makefile:2163: recipe for target 'check-am' failed
> make[2]: Leaving directory '/??PKGBUILDDIR??'
> make[1]: *** [check] Error 2
> Makefile:2166: recipe for target 'check' failed
> make[1]: Leaving directory '/??PKGBUILDDIR??'
> dh_auto_test: make -j1 check returned exit code 2
> make: *** [build-arch] Error 2
> debian/rules:8: recipe for target 'build-arch' failed
> dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
> 

> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging


-- 
http://fam-tille.de