[Debian-med-packaging] Bug#795239: progressivemauve: FTBFS: undefined reference to `mems::gnAlignedSequences::getSupportedFormats[abi:cxx11]()' (and others)

[Andreas Tille]

Hi Martin,

I suspect I need to do a g5 transition for libmems.  Could you confirm
this suspicion and I'll do as I did for libgenome.

Kind regards

        Andreas.

On Wed, Aug 12, 2015 at 10:10:15AM +0200, Martin Pitt wrote:
> Package: progressivemauve
> Severity: serious
> Version: 1.2.0+4713-1
> 
> This package currently FTBFS in sid:
> 
> | g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize   -DCOMMAND_LINE  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize    -Wl,-z,relro -o mauveAligner mauveAligner.o -lMems-1.6 -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread  -lGenome-1.3 -lMUSCLE-3.7    
> | mauveAligner.o: In function `print_usage(char const*)':
> | /«BUILDDIR»/progressivemauve-1.2.0+4713/src/mauveAligner.cpp:909: undefined reference to `mems::gnAlignedSequences::getSupportedFormats[abi:cxx11]()'
> | mauveAligner.o: In function `doAlignment(int, char**)':
> | /«BUILDDIR»/progressivemauve-1.2.0+4713/src/mauveAligner.cpp:376: undefined reference to `mems::MuscleInterface::SetExtraMuscleArguments(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
> | /«BUILDDIR»/progressivemauve-1.2.0+4713/src/mauveAligner.cpp:365: undefined reference to `mems::FileSML::registerTempPath(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
> 
> (Many more errors). Full build log attached for convenience.
> 
> Thanks,
> 
> Martin
> 
> -- 
> Martin Pitt                        | http://www.piware.de
> Ubuntu Developer (www.ubuntu.com)  | Debian Developer  (www.debian.org)


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