Your message dated Tue, 12 Jul 2016 07:34:39 +0000
with message-id <e1bmsdh-0000tg...@franck.debian.org>
and subject line Bug#811815: fixed in murasaki 1.68.6-6
has caused the Debian Bug report #811815,
regarding murasaki: FTBFS with GCC 6: no match for
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.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
811815: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811815
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: murasaki
Version: 1.68.6-4
Severity: important
User: debian-...@lists.debian.org
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,
> ^~~~~~~~
--- End Message ---
--- Begin Message ---
Source: murasaki
Source-Version: 1.68.6-6
We believe that the bug you reported is fixed in the latest version of
murasaki, which is due to be installed in the Debian FTP archive.
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 811...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Gert Wollny <gw.foss...@gmail.com> (supplier of updated murasaki 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 30 Jun 2016 09:15:01 +0000
Source: murasaki
Binary: murasaki murasaki-mpi murasaki-common
Architecture: source all amd64
Version: 1.68.6-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Gert Wollny <gw.foss...@gmail.com>
Description:
murasaki - homology detection tool across multiple large genomes
murasaki-common - homology detection tool across multiple large genomes
(common fil
murasaki-mpi - homology detection tool across multiple large genomes
(MPI-versio
Closes: 811815
Changes:
murasaki (1.68.6-6) unstable; urgency=medium
.
[ Gert Wollny ]
* Team upload
* d/p/gcc-6: Add patch to compile with gcc-6: Closes: #811815
* cme fix dpkg-control
.
[ Andreas Tille ]
* hardening=+bindnow
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murasaki-mpi-dbgsym_1.68.6-6_amd64.deb
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murasaki_1.68.6-6_amd64.deb
Files:
6f0f57921f3fedfbce472fb08eb98c85 2213 science optional murasaki_1.68.6-6.dsc
7560c5f08cc459d967bea0af2abd84de 6920 science optional
murasaki_1.68.6-6.debian.tar.xz
696bb49f7d4eda6c513618854941d07a 144196 science optional
murasaki-common_1.68.6-6_all.deb
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murasaki-dbgsym_1.68.6-6_amd64.deb
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murasaki-mpi-dbgsym_1.68.6-6_amd64.deb
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murasaki-mpi_1.68.6-6_amd64.deb
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murasaki_1.68.6-6_amd64.deb
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