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

Matthias Klose doko at debian.org
Thu Feb 12 10:32:46 UTC 2015

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:
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

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