Your message dated Thu, 30 Jun 2016 11:18:09 +0100
with message-id <[email protected]>
and subject line Re: bamtools: FTBFS with GCC 6: no matching function for call
to
has caused the Debian Bug report #811856,
regarding bamtools: FTBFS with GCC 6: no matching function for call to
to be marked as done.
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If this is not the case it is now your responsibility to reopen the
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--
811856: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811856
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: bamtools
Version: 2.4.0+dfsg-3
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
...
> [ 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
--- End Message ---
--- Begin Message ---
This has been fixed in 2.4.0+dfsg-4 but apparently this bug was never
closed. I can confirm that the package builds fine from source for me
using GCC 6.1.1.
Thanks
Sascha
On Tue, 19 Jan 2016 18:46:48 -0800 Martin Michlmayr <[email protected]> wrote:
> Package: bamtools
> Version: 2.4.0+dfsg-3
> 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
> ...
> > [ 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) );
> > ^~~~
--
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--- End Message ---
