[Debian-med-packaging] Bug#811859: berkeley-express: FTBFS with GCC 6: no matching function for call to

[Martin Michlmayr]

Package: berkeley-express
Version: 1.5.1-1
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
...
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++    -I/usr/include/bamtools  -Wall -O3 -DNDEBUG   -o CMakeFiles/express.dir/sequence.cpp.o -c /<<PKGBUILDDIR>>/src/sequence.cpp
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++    -I/usr/include/bamtools  -Wall -O3 -DNDEBUG   -o CMakeFiles/express.dir/bundles.cpp.o -c /<<PKGBUILDDIR>>/src/bundles.cpp
> [ 94%] Building CXX object src/CMakeFiles/express.dir/alignments.pb.cc.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++    -I/usr/include/bamtools  -Wall -O3 -DNDEBUG   -o CMakeFiles/express.dir/targets.pb.cc.o -c /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/targets.pb.cc
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++    -I/usr/include/bamtools  -Wall -O3 -DNDEBUG   -o CMakeFiles/express.dir/alignments.pb.cc.o -c /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/alignments.pb.cc
> In file included from /<<PKGBUILDDIR>>/src/main.cpp:42:0:
> /<<PKGBUILDDIR>>/src/update_check.h: In function 'bool get_current_version(char*)':
> /<<PKGBUILDDIR>>/src/update_check.h:89:28: warning: argument to 'sizeof' in 'void bzero(void*, size_t)' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess]
>   bzero(curr_version, sizeof(curr_version));
>                             ^
> 
> /<<PKGBUILDDIR>>/src/targets.cpp: In member function 'double Target::sample_likelihood(bool, const std::vector<const Target*>*) const':
> /<<PKGBUILDDIR>>/src/targets.cpp:116:62: error: no matching function for call to 'Target::cached_effective_length(const boost::shared_ptr<BiasBoss>&) const'
>    double tot_eff_len = cached_effective_length(lib.bias_table);
>                                                               ^
> 
> In file included from /<<PKGBUILDDIR>>/src/targets.cpp:10:0:
> /<<PKGBUILDDIR>>/src/targets.h:399:10: note: candidate: double Target::cached_effective_length(bool) const
>    double cached_effective_length(bool with_bias=true) const;
>           ^~~~~~~~~~~~~~~~~~~~~~~
> 
> /<<PKGBUILDDIR>>/src/targets.h:399:10: note:   no known conversion for argument 1 from 'const boost::shared_ptr<BiasBoss>' to 'bool'
> /<<PKGBUILDDIR>>/src/targets.cpp:121:77: error: no matching function for call to 'Target::cached_effective_length(const boost::shared_ptr<BiasBoss>&) const'
>                              neighbor->cached_effective_length(lib.bias_table));
>                                                                              ^
> 
> In file included from /<<PKGBUILDDIR>>/src/targets.cpp:10:0:
> /<<PKGBUILDDIR>>/src/targets.h:399:10: note: candidate: double Target::cached_effective_length(bool) const
>    double cached_effective_length(bool with_bias=true) const;
>           ^~~~~~~~~~~~~~~~~~~~~~~
> 
> /<<PKGBUILDDIR>>/src/targets.h:399:10: note:   no known conversion for argument 1 from 'const boost::shared_ptr<BiasBoss>' to 'bool'
> src/CMakeFiles/express.dir/build.make:225: recipe for target 'src/CMakeFiles/express.dir/targets.cpp.o' failed
> make[3]: *** [src/CMakeFiles/express.dir/targets.cpp.o] Error 1

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