Your message dated Thu, 30 Jun 2016 16:44:34 +0000
with message-id <e1bif4s-0007dr...@franck.debian.org>
and subject line Bug#811870: fixed in libmems 1.6.0+4725-3
has caused the Debian Bug report #811870,
regarding libmems: FTBFS with GCC 6: no matching function for call to
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
811870: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811870
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: libmems
Version: 1.6.0+4725-2
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
...
> /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I..
> -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer
> -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7
> -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o
> ProgressiveAligner.lo ProgressiveAligner.cpp
> libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
> -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security -c
> ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o
> In file included from /usr/include/c++/6/ext/hash_map:60:0,
> from ../libMems/HomologyHMM/dptables.h:43,
> from ../libMems/HomologyHMM/homology.h:27,
> from ../libMems/Islands.h:25,
> from ../libMems/ProgressiveAligner.h:21,
> from ProgressiveAligner.cpp:14:
> /usr/include/c++/6/backward/backward_warning.h:32:2: warning: #warning This
> file includes at least one deprecated or antiquated header which may be
> removed without further notice at a future date. Please use a non-deprecated
> interface with equivalent functionality instead. For a listing of replacement
> headers and interfaces, consult the file backward_warning.h. To disable this
> warning use -Wno-deprecated. [-Wcpp]
> #warning \
> ^~~~~~~
>
> ProgressiveAligner.cpp: In member function 'void
> mems::ProgressiveAligner::constructLcbTrackingMatches(node_id_t,
> std::vector<mems::AbstractMatch*>&,
> std::vector<mems::LcbTrackingMatch<mems::AbstractMatch*> >&)':
> ProgressiveAligner.cpp:1602:74: error: no matching function for call to
> 'std::vector<boost::tuples::tuple<mems::CompactGappedAlignment<>*,
> std::vector<boost::dynamic_bitset<> >*, mems::AbstractMatch*>
> >::push_back(std::tuple<mems::CompactGappedAlignment<mems::AbstractGappedAlignment<mems::HybridAbstractMatch<2u,
> std::allocator<long long int>, std::allocator<unsigned int> > > >*,
> std::vector<boost::dynamic_bitset<long unsigned int, std::allocator<long
> unsigned int> >, std::allocator<boost::dynamic_bitset<long unsigned int,
> std::allocator<long unsigned int> > > >*, mems::AbstractMatch*>)'
> cga_list.push_back(make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI]));
> ^
>
> In file included from /usr/include/c++/6/vector:64:0,
> from ../libMems/AbstractMatch.h:17,
> from ../libMems/SparseAbstractMatch.h:18,
> from ../libMems/Interval.h:18,
> from ../libMems/SuperInterval.h:8,
> from ../libMems/ProgressiveAligner.h:16,
> from ProgressiveAligner.cpp:14:
> /usr/include/c++/6/bits/stl_vector.h:914:7: note: candidate: void
> std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp =
> boost::tuples::tuple<mems::CompactGappedAlignment<>*,
> std::vector<boost::dynamic_bitset<> >*, mems::AbstractMatch*>; _Alloc =
> std::allocator<boost::tuples::tuple<mems::CompactGappedAlignment<>*,
> std::vector<boost::dynamic_bitset<> >*, mems::AbstractMatch*> >;
> std::vector<_Tp, _Alloc>::value_type =
> boost::tuples::tuple<mems::CompactGappedAlignment<>*,
> std::vector<boost::dynamic_bitset<> >*, mems::AbstractMatch*>]
> push_back(const value_type& __x)
> ^~~~~~~~~
>
> /usr/include/c++/6/bits/stl_vector.h:914:7: note: no known conversion for
> argument 1 from
> 'std::tuple<mems::CompactGappedAlignment<mems::AbstractGappedAlignment<mems::HybridAbstractMatch<2u,
> std::allocator<long long int>, std::allocator<unsigned int> > > >*,
> std::vector<boost::dynamic_bitset<long unsigned int, std::allocator<long
> unsigned int> >, std::allocator<boost::dynamic_bitset<long unsigned int,
> std::allocator<long unsigned int> > > >*, mems::AbstractMatch*>' to 'const
> value_type& {aka const boost::tuples::tuple<mems::CompactGappedAlignment<>*,
> std::vector<boost::dynamic_bitset<> >*, mems::AbstractMatch*>&}'
> /usr/include/c++/6/bits/stl_vector.h:932:7: note: candidate: void
> std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&)
> [with _Tp = boost::tuples::tuple<mems::CompactGappedAlignment<>*,
> std::vector<boost::dynamic_bitset<> >*, mems::AbstractMatch*>; _Alloc =
> std::allocator<boost::tuples::tuple<mems::CompactGappedAlignment<>*,
> std::vector<boost::dynamic_bitset<> >*, mems::AbstractMatch*> >;
> std::vector<_Tp, _Alloc>::value_type =
> boost::tuples::tuple<mems::CompactGappedAlignment<>*,
> std::vector<boost::dynamic_bitset<> >*, mems::AbstractMatch*>]
> push_back(value_type&& __x)
> ^~~~~~~~~
>
> /usr/include/c++/6/bits/stl_vector.h:932:7: note: no known conversion for
> argument 1 from
> 'std::tuple<mems::CompactGappedAlignment<mems::AbstractGappedAlignment<mems::HybridAbstractMatch<2u,
> std::allocator<long long int>, std::allocator<unsigned int> > > >*,
> std::vector<boost::dynamic_bitset<long unsigned int, std::allocator<long
> unsigned int> >, std::allocator<boost::dynamic_bitset<long unsigned int,
> std::allocator<long unsigned int> > > >*, mems::AbstractMatch*>' to
> 'std::vector<boost::tuples::tuple<mems::CompactGappedAlignment<>*,
> std::vector<boost::dynamic_bitset<> >*, mems::AbstractMatch*> >::value_type&&
> {aka boost::tuples::tuple<mems::CompactGappedAlignment<>*,
> std::vector<boost::dynamic_bitset<> >*, mems::AbstractMatch*>&&}'
> Makefile:765: recipe for target 'ProgressiveAligner.lo' failed
--
Martin Michlmayr
Linux for HPE Helion, Hewlett Packard Enterprise
--- End Message ---
--- Begin Message ---
Source: libmems
Source-Version: 1.6.0+4725-3
We believe that the bug you reported is fixed in the latest version of
libmems, 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 libmems 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 13:30:08 +0000
Source: libmems
Binary: libmems-1.6-dev libmems-1.6-1v5
Architecture: source amd64
Version: 1.6.0+4725-3
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:
libmems-1.6-1v5 - library to support DNA string matching and comparative
genomics
libmems-1.6-dev - development library to support DNA string matching and
comparativ
Closes: 811870
Changes:
libmems (1.6.0+4725-3) unstable; urgency=medium
.
[ Gert Wollny ]
* Team upload
* d/p/05: Add patch to fix compilation with g++-6, Closes: #811870
* d/control: cme fix dpkg-control
.
[ Andreas Tille ]
* Set source section to science
* hardening=+bindnow
* drop unneeded overrides for d-shlibmove
Checksums-Sha1:
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libmems_1.6.0+4725-3.debian.tar.xz
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libmems-1.6-1v5-dbgsym_1.6.0+4725-3_amd64.deb
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libmems-1.6-1v5_1.6.0+4725-3_amd64.deb
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libmems-1.6-dev_1.6.0+4725-3_amd64.deb
Checksums-Sha256:
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Files:
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20500b06b06400dbb3ace37ac96f3f9e 7252 science optional
libmems_1.6.0+4725-3.debian.tar.xz
932f92ba88193c5e5f1d9f49fc1b2798 7223892 debug extra
libmems-1.6-1v5-dbgsym_1.6.0+4725-3_amd64.deb
27f7f8485a00e984830a26c60174affc 668624 libs optional
libmems-1.6-1v5_1.6.0+4725-3_amd64.deb
fe2005996800c3a218ee710e0ea09b78 965732 libdevel optional
libmems-1.6-dev_1.6.0+4725-3_amd64.deb
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