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: [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
> ...
> > /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
>
> _______________________________________________
> Debian-med-packaging mailing list
> [email protected]
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
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