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
