[Debian-med-packaging] Bug#811870: libmems: FTBFS with GCC 6: no matching function for call to

[Andreas Tille]

Hi Aaron,

as you can see below libmems fails to build from source when using gcc 6
due to stricter type checking.  Feel free to contact us via the bug
e-mail (in To:) if you have any questions.

Kind regards

      Andreas.

On Tue, Jan 19, 2016 at 06:51:23PM -0800, Martin Michlmayr wrote:
> Package: libmems
> Version: 1.6.0+4725-2
> Severity: important
> User: debian-gcc at 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
> 
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