[Debian-med-packaging] Bug#811881: tophat: FTBFS with GCC 6: no matching function for call to

[Martin Michlmayr]

Package: tophat
Version: 2.1.0+dfsg-1
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
...
> g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -c -o tophat_reports.o tophat_reports.cpp
> In file included from tophat_reports.cpp:36:0:
> common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)':
> common.h:579:14: warning: variable 'pre_block_offs' set but not used [-Wunused-but-set-variable]
>       int     pre_block_offs=0; //but before this write()
>               ^~~~~~~~~~~~~~
> 
> tophat_reports.cpp: In member function 'void ReportWorker::write_singleton_alignments(uint64_t, HitsForRead&, ReadStream&, GBamWriter&, FragmentType, GetReadProc*, QReadData)':
> tophat_reports.cpp:2292:8: warning: variable 'map_code' set but not used [-Wunused-but-set-variable]
>    char map_code=0;
>         ^~~~~~~~
> 
> tophat_reports.cpp: In function 'void driver(const string&, std::istream&, const std::vector<std::__cxx11::basic_string<char> >&, const string&, const std::vector<std::__cxx11::basic_string<char> >&, const string&, FILE*, FILE*, FILE*, FILE*)':
> tophat_reports.cpp:2707:128: error: no matching function for call to 'make_pair(Junction, JunctionStats&)'
>      gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
>                                                                                                                                 ^
> 
> In file included from /usr/include/c++/6/bits/stl_algobase.h:64:0,
>                  from /usr/include/c++/6/vector:60,
>                  from tophat_reports.cpp:20:
> /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:
> tophat_reports.cpp:2707:128: note:   cannot convert 'junction_stat' (type 'JunctionStats') to type 'JunctionStats&&'
>      gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
>                                                                                                                                 ^
> 
> Makefile:1453: recipe for target 'tophat_reports.o' failed
> make[3]: *** [tophat_reports.o] Error 1

-- 
Martin Michlmayr
Linux for HPE Helion, Hewlett Packard Enterprise