[Debian-med-packaging] Bug#811911: kmer-tools: FTBFS with GCC 6: declared in this scope

[Martin Michlmayr]

Package: kmer-tools
Version: 0~20150903+r2013-1
Severity: important
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-6 gcc-6-not-declared

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
...
> tapper/tagger.C:362:73: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
>        fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n",
>                                                                          ^
> 
> In file included from /usr/include/c++/6/cmath:44:0,
>                  from /usr/include/c++/6/random:38,
>                  from /usr/include/c++/6/bits/stl_algo.h:66,
>                  from /usr/include/c++/6/algorithm:62,
>                  from /<<BUILDDIR>>/kmer-tools-0~20150903+r2013/libutil/intervalList.H:4,
>                  from /<<BUILDDIR>>/kmer-tools-0~20150903+r2013/libutil/util++.H:40,
>                  from /<<BUILDDIR>>/kmer-tools-0~20150903+r2013/libbio/bio++.H:15,
>                  from tapper/tapperTag.H:1,
>                  from tapper/tagger.C:1:
> tapper/tapperResult.H:574:16: error: expected unqualified-id before numeric constant
>    recordFile  *SING;
>                 ^
> 
> In file included from tapper/tagger.C:2:0:
> tapper/tapperResult.H:574:15: error: expected ';' at end of member declaration
>    recordFile  *SING;
>                ^
> 
> In file included from /usr/include/c++/6/cmath:44:0,
>                  from /usr/include/c++/6/random:38,
>                  from /usr/include/c++/6/bits/stl_algo.h:66,
>                  from /usr/include/c++/6/algorithm:62,
>                  from /<<BUILDDIR>>/kmer-tools-0~20150903+r2013/libutil/intervalList.H:4,
>                  from /<<BUILDDIR>>/kmer-tools-0~20150903+r2013/libutil/util++.H:40,
>                  from /<<BUILDDIR>>/kmer-tools-0~20150903+r2013/libbio/bio++.H:15,
>                  from tapper/tapperTag.H:1,
>                  from tapper/tagger.C:1:
> tapper/tapperResult.H:574:16: error: expected unqualified-id before numeric constant
>    recordFile  *SING;
>                 ^
> 
> In file included from tapper/tagger.C:2:0:
> tapper/tapperResult.H: In constructor 'tapperResultFile::tapperResultFile(char*, char)':
> tapper/tapperResult.H:420:74: error: lvalue required as left operand of assignment
>      SING = new recordFile(filename, 0, sizeof(tapperResultFragment), mode);
>                                                                           ^
> 
> In file included from /usr/include/c++/6/cmath:44:0,
>                  from /usr/include/c++/6/random:38,
>                  from /usr/include/c++/6/bits/stl_algo.h:66,
>                  from /usr/include/c++/6/algorithm:62,
>                  from /<<BUILDDIR>>/kmer-tools-0~20150903+r2013/libutil/intervalList.H:4,
>                  from /<<BUILDDIR>>/kmer-tools-0~20150903+r2013/libutil/util++.H:40,
>                  from /<<BUILDDIR>>/kmer-tools-0~20150903+r2013/libbio/bio++.H:15,
>                  from tapper/tapperTag.H:1,
>                  from tapper/tagger.C:1:
> tapper/tapperResult.H: In destructor 'tapperResultFile::~tapperResultFile()':
> tapper/tapperResult.H:438:12: error: type 'int' argument given to 'delete', expected pointer
>      delete SING;
>             ^
> 
> In file included from tapper/tagger.C:2:0:
> tapper/tapperResult.H: In member function 'bool tapperResultFile::read(tapperResult*)':
> tapper/tapperResult.H:527:13: error: base operand of '->' is not a pointer
>      if (SING->getRecord(align->sing, align->idx._numFragSingleton) != align->idx._numFragSingleton)
>              ^~
> 
> tapper/tapperResult.H: In member function 'void tapperResultFile::write(tapperResultIndex*, tapperResultFragment*, tapperResultFragment*, tapperResultFragment*, tapperResultMated*, tapperResultTangled*, uint32*)':
> tapper/tapperResult.H:556:9: error: base operand of '->' is not a pointer
>      SING->putRecord(sing, idx->_numFragSingleton);