Hi Kris, I'm not sure whether you are aware that murasaki is packaged for Debian by the Debian Med team. Over time we collected a set of patches you might be interested in:
https://anonscm.debian.org/viewvc/debian-med/trunk/packages/murasaki/trunk/debian/patches/ We have not yet developed a patch for the build issue with gcc 6 you can read below. Feel free to contact us about the problem via the bug report e-mail if you have any questions. Kind regards and thanks for providing murasaki as Free Software Andreas. On Tue, Jan 19, 2016 at 06:16:57PM -0800, Martin Michlmayr wrote: > Package: murasaki > Version: 1.68.6-4 > Severity: important > User: [email protected] > Usertags: ftbfs-gcc-6 gcc-6-no-match > > This package fails to build with GCC 6. GCC 6 has not been released > yet, but it's expected that GCC 6 will become the default compiler for > stretch. > > Note that only the first error is reported; there might be more. You > can find a snapshot of GCC 6 in experimental. To build with GCC 6, > you can set CC=gcc-6 CXX=g++-6 explicitly. > > You may be able to find out more about this issue at > https://gcc.gnu.org/gcc-6/changes.html > > > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux > ... > > mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g > > -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV > > -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c dinkymath.cc > > In file included from /usr/lib/openmpi/include/mpi.h:253:0, > > from murasaki_mpi.h:33, > > from shmvector.hh:30, > > from sequence.h:44, > > from murasaki.h:24, > > from dinkymath.cc:27: > > /usr/lib/openmpi/include/mpi_portable_platform.h:374:34: warning: invalid > > suffix on literal; C++11 requires a space between literal and string macro > > [-Wliteral-suffix] > > > > _STRINGIFY(__GNUC__)"."_STRINGIFY(__GNUC_MINOR__)"."_STRINGIFY(__GNUC_PATCHLEVEL__) > > ^ > > > > /usr/lib/openmpi/include/mpi_portable_platform.h:374:63: warning: invalid > > suffix on literal; C++11 requires a space between literal and string macro > > [-Wliteral-suffix] > > > > _STRINGIFY(__GNUC__)"."_STRINGIFY(__GNUC_MINOR__)"."_STRINGIFY(__GNUC_PATCHLEVEL__) > > ^ > > > > dinkymath.cc: In function 'std::__cxx11::string littleEndianStr(unsigned > > int, int)': > > dinkymath.cc:40:7: warning: variable 'last' set but not used > > [-Wunused-but-set-variable] > > int last=0; > > ^~~~ > > > > dinkymath.cc: In function 'std::__cxx11::string littleEndianPat(unsigned > > int, int)': > > dinkymath.cc:53:7: warning: variable 'last' set but not used > > [-Wunused-but-set-variable] > > int last=0; > > ^~~~ > > > > mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g > > -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV > > -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c sequence.cc > > In file included from /usr/lib/openmpi/include/mpi.h:253:0, > > from murasaki_mpi.h:33, > > from shmvector.hh:30, > > from sequence.h:44, > > from murasaki.h:24, > > from sequence.cc:28: > > /usr/lib/openmpi/include/mpi_portable_platform.h:374:34: warning: invalid > > suffix on literal; C++11 requires a space between literal and string macro > > [-Wliteral-suffix] > > > > _STRINGIFY(__GNUC__)"."_STRINGIFY(__GNUC_MINOR__)"."_STRINGIFY(__GNUC_PATCHLEVEL__) > > ^ > > > > /usr/lib/openmpi/include/mpi_portable_platform.h:374:63: warning: invalid > > suffix on literal; C++11 requires a space between literal and string macro > > [-Wliteral-suffix] > > > > _STRINGIFY(__GNUC__)"."_STRINGIFY(__GNUC_MINOR__)"."_STRINGIFY(__GNUC_PATCHLEVEL__) > > ^ > > > > sequence.cc: In destructor 'Sequence::~Sequence()': > > sequence.cc:377:123: warning: throw will always call terminate() > > [-Wterminate] > > throw MurasakiException("Couldn't mark System V IPC shared memory region > > for deletion for sequence "+name+strerror(errno)); > > > > ^ > > > > sequence.cc:377:123: note: in C++11 destructors default to noexcept > > sequence.cc: In destructor 'BitSequence::~BitSequence()': > > sequence.cc:1394:133: warning: throw will always call terminate() > > [-Wterminate] > > throw MurasakiException("Couldn't detach System V shared memory region > > for "+(seq ? seq->filename:string("(anon)"))+strerror(errno)); > > > > ^ > > > > sequence.cc:1394:133: note: in C++11 destructors default to noexcept > > sequence.cc: In member function 'void Hash::writeHistogram(std::ostream&)': > > sequence.cc:2048:8: error: no match for 'operator!=' (operand types are > > 'std::ostream {aka std::basic_ostream<char>}' and 'std::ostream {aka > > std::basic_ostream<char>}') > > if(of!=cerr) > > ~~^~~~~~ > > > > sequence.cc:2048:8: note: candidate: operator!=(int, int) <built-in> > > sequence.cc:2048:8: note: no known conversion for argument 2 from > > 'std::ostream {aka std::basic_ostream<char>}' to 'int' > > In file included from /usr/include/c++/6/bits/stl_algobase.h:67:0, > > from /usr/include/c++/6/bits/stl_tree.h:63, > > from /usr/include/c++/6/set:60, > > from cmultiset.h:33, > > from sequence.h:30, > > from murasaki.h:24, > > from sequence.cc:28: > > /usr/include/c++/6/bits/stl_iterator.h:863:5: note: candidate: > > template<class _IteratorL, class _IteratorR, class _Container> bool > > __gnu_cxx::operator!=(const __gnu_cxx::__normal_iterator<_IteratorL, > > _Container>&, const __gnu_cxx::__normal_iterator<_IteratorR, _Container>&) > > operator!=(const __normal_iterator<_IteratorL, _Container>& __lhs, > > ^~~~~~~~ > > _______________________________________________ > Debian-med-packaging mailing list > [email protected] > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de
