[Debian-med-packaging] Bug#811856: bamtools: FTBFS with GCC 6: no matching function for call to
Martin Michlmayr
tbm at hpe.com
Wed Jan 20 02:46:48 UTC 2016
Package: bamtools
Version: 2.4.0+dfsg-3
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
...
> [ 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
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