[Debian-med-packaging] Bug#812294: bedtools: FTBFS with GCC 6: parse error in template argument

[Martin Michlmayr]

Package: bedtools
Version: 2.25.0-1
Severity: normal
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-6

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.

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
...
> - Building in src/utils/bedFile
>   * compiling bedFile.cpp
> In file included from bedFile.cpp:12:0:
> bedFile.h: In member function 'bool BedFile::parseVcfLine(T&, const std::vector<std::__cxx11::basic_string<char> >&)':
> bedFile.h:799:47: error: parse error in template argument list
>              else if ( (bed.start < 0) || (bed.end < 0) ) {
>                                                ^~~~~~~
> 
> bedFile.h: In member function 'bool BedFile::parseGffLine(T&, const std::vector<std::__cxx11::basic_string<char> >&)':
> bedFile.h:877:42: error: parse error in template argument list
>              if ( (bed.start < 0) || (bed.end < 0) ) {
>                                           ^~~~~~~
> 
> bedFile.h: In instantiation of 'bool BedFile::parseVcfLine(T&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = BED]':
> bedFile.h:567:55:   required from 'BedLineStatus BedFile::parseLine(T&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = BED]'
> bedFile.cpp:233:44:   required from here
> bedFile.h:799:47: error: 'end' is not a member template function
>              else if ( (bed.start < 0) || (bed.end < 0) ) {
>                                           ~~~~~^~~~~~~~
> 
> bedFile.h: In instantiation of 'bool BedFile::parseGffLine(T&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = BED]':
> bedFile.h:572:55:   required from 'BedLineStatus BedFile::parseLine(T&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = BED]'
> bedFile.cpp:233:44:   required from here
> bedFile.h:877:42: error: 'end' is not a member template function
>              if ( (bed.start < 0) || (bed.end < 0) ) {
>                                      ~~~~~^~~~~~~~
> 
> Makefile:22: recipe for target '../../../obj//bedFile.o' failed
> make[2]: *** [../../../obj//bedFile.o] Error 1

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