Package: bamtools Version: 2.4.0+dfsg-3 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 ... > [ 98%] Building CXX object > src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o > cd /<<BUILDDIR>>/bamtools-2.4.0+dfsg/obj-x86_64-linux-gnu/src/toolkit && > /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -I/<<BUILDDIR>>/bamtools-2.4.0+dfsg/src > -I/<<BUILDDIR>>/bamtools-2.4.0+dfsg/obj-x86_64-linux-gnu/include > -I/<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/api > -I/<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/utils -g -O2 > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o > CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o -c > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_count.cpp > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp: In member > function 'bool > BamTools::ResolveTool::ReadNamesFileReader::Read(std::map<std::__cxx11::basic_string<char>, > ReadGroupResolver>&)': > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp:413:74: > error: no matching function for call to > 'make_pair(__gnu_cxx::__alloc_traits<std::allocator<std::__cxx11::basic_string<char> > > >::value_type&, bool)' > resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) > ; > ^ > > In file included from /usr/include/c++/6/bits/stl_algobase.h:64:0, > from /usr/include/c++/6/bits/char_traits.h:39, > from /usr/include/c++/6/string:40, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_tool.h:14, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.h:13, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp:10: > /usr/include/c++/6/bits/stl_pair.h:406:5: note: candidate: template<class > _T1, class _T2> constexpr std::pair<typename > std::__decay_and_strip<_Tp>::__type, typename > std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) > make_pair(_T1&& __x, _T2&& __y) > ^~~~~~~~~ > > /usr/include/c++/6/bits/stl_pair.h:406:5: note: template argument > deduction/substitution failed: > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp:413:74: > note: cannot convert 'fields.std::vector<_Tp, > _Alloc>::operator[]<std::__cxx11::basic_string<char>, > std::allocator<std::__cxx11::basic_string<char> > >(1ul)' (type > '__gnu_cxx::__alloc_traits<std::allocator<std::__cxx11::basic_string<char> > > >::value_type {aka std::__cxx11::basic_string<char>}') to type > 'std::__cxx11::basic_string<char>&&' > resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) > ; > ^ > > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp: In member > function 'bool > BamTools::ResolveTool::StatsFileReader::ParseReadGroupLine(const string&, > std::map<std::__cxx11::basic_string<char>, ReadGroupResolver>&)': > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp:610:75: > error: no matching function for call to 'make_pair(const string&, > ReadGroupResolver&)' > readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) > ); > ^ > > In file included from /usr/include/c++/6/bits/stl_algobase.h:64:0, > from /usr/include/c++/6/bits/char_traits.h:39, > from /usr/include/c++/6/string:40, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_tool.h:14, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.h:13, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp:10: > /usr/include/c++/6/bits/stl_pair.h:406:5: note: candidate: template<class > _T1, class _T2> constexpr std::pair<typename > std::__decay_and_strip<_Tp>::__type, typename > std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) > make_pair(_T1&& __x, _T2&& __y) > ^~~~~~~~~ > > /usr/include/c++/6/bits/stl_pair.h:406:5: note: template argument > deduction/substitution failed: > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp:610:61: > note: cannot convert 'name' (type 'const string {aka const > std::__cxx11::basic_string<char>}') to type > 'std::__cxx11::basic_string<char>&&' > readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) > ); > ^~~~ > > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp: In member > function 'bool BamTools::ResolveTool::ResolveToolPrivate::MakeStats()': > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp:1017:93: > error: no matching function for call to 'make_pair(std::__cxx11::string&, > const bool&)' > else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, > isCurrentMateUnique) ); > > ^ > > In file included from /usr/include/c++/6/bits/stl_algobase.h:64:0, > from /usr/include/c++/6/bits/char_traits.h:39, > from /usr/include/c++/6/string:40, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_tool.h:14, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.h:13, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp:10: > /usr/include/c++/6/bits/stl_pair.h:406:5: note: candidate: template<class > _T1, class _T2> constexpr std::pair<typename > std::__decay_and_strip<_Tp>::__type, typename > std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) > make_pair(_T1&& __x, _T2&& __y) > ^~~~~~~~~ > > /usr/include/c++/6/bits/stl_pair.h:406:5: note: template argument > deduction/substitution failed: > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp:1017:68: > note: cannot convert 'al.BamTools::BamAlignment::Name' (type > 'std::__cxx11::string {aka std::__cxx11::basic_string<char>}') to type > 'std::__cxx11::basic_string<char>&&' > else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, > isCurrentMateUnique) ); > ~~~^~~~ > > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp: In member > function 'void BamTools::ResolveTool::ResolveToolPrivate::ParseHeader(const > BamTools::SamHeader&)': > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp:1049:93: > error: no matching function for call to 'make_pair(const string&, > ReadGroupResolver)' > m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, > ReadGroupResolver()) ); > > ^ > > In file included from /usr/include/c++/6/bits/stl_algobase.h:64:0, > from /usr/include/c++/6/bits/char_traits.h:39, > from /usr/include/c++/6/string:40, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_tool.h:14, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.h:13, > from > /<<BUILDDIR>>/bamtools-2.4.0+dfsg/src/toolkit/bamtools_resolve.cpp:10: > /usr/include/c++/6/bits/stl_pair.h:406:5: note: candidate: template<class > _T1, class _T2> constexpr std::pair<typename > std::__decay_and_strip<_Tp>::__type, typename > std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) > make_pair(_T1&& __x, _T2&& __y) > ^~~~~~~~~ -- Martin Michlmayr Linux for HPE Helion, Hewlett Packard Enterprise
