[Debian-med-packaging] Bug#868919: physamp: FTBFS: AlignmentOptimizer.cpp:39:32: fatal error: Bpp/Seq/Alphabet.all: No such file or directory

[Julien Yann Dutheil]

Dear Andreas,

Yes, should be. But I noticed some other problems... I have made a version
1.0.2 addressing them. Then I synchronized the upstream branch accordingly,
and then merged the master branch and the upstream branch, is that the
correct way to do? Version 1.0.2-1 should then normally build fine.

I also committed a patch for bppsuite on x32 arch. Will now work on
maffilter.

Best,

Julien.

On Wed, Jul 19, 2017 at 6:15 PM, Andreas Tille <andreas at fam-tille.de> wrote:

> Hi Julien,
>
> I guess this issue is connected to our latest changes in the library
> packages.
>
> Kind regards
>
>         Andreas.
>
> On Wed, Jul 19, 2017 at 05:52:18PM +0200, Lucas Nussbaum wrote:
> > Source: physamp
> > Version: 0.2.0-1
> > Severity: serious
> > Tags: buster sid
> > User: debian-qa at lists.debian.org
> > Usertags: qa-ftbfs-20170719 qa-ftbfs
> > Justification: FTBFS on amd64
> >
> > Hi,
> >
> > During a rebuild of all packages in sid, your package failed to build on
> > amd64.
> >
> > Relevant part (hopefully):
> > > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/physamp && /usr/bin/c++
>  -Wall -Weffc++ -Wshadow -Wconversion   -o CMakeFiles/bppalnoptim.dir/AlignmentOptimizer.cpp.o
> -c /<<PKGBUILDDIR>>/physamp/AlignmentOptimizer.cpp
> > > /<<PKGBUILDDIR>>/physamp/AlignmentOptimizer.cpp:39:32: fatal error:
> Bpp/Seq/Alphabet.all: No such file or directory
> > >  #include <Bpp/Seq/Alphabet.all>
> > >                                 ^
> > > compilation terminated.
> > > physamp/CMakeFiles/bppalnoptim.dir/build.make:65: recipe for target
> 'physamp/CMakeFiles/bppalnoptim.dir/AlignmentOptimizer.cpp.o' failed
> > > make[3]: *** [physamp/CMakeFiles/bppalnoptim.dir/AlignmentOptimizer.cpp.o]
> Error 1
> >
> > The full build log is available from:
> >    http://aws-logs.debian.net/2017/07/19/physamp_0.2.0-1_unstable.log
> >
> > A list of current common problems and possible solutions is available at
> > http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to
> contribute!
> >
> > About the archive rebuild: The rebuild was done on EC2 VM instances from
> > Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> > failed build was retried once to eliminate random failures.
> >
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at lists.alioth.debian.org
> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/
> debian-med-packaging
> >
>
> --
> http://fam-tille.de
>



-- 
Julien Y. Dutheil, Ph-D
0 (+49) 6421 178 986

§ Max Planck Institute for Evolutionary Biology
Molecular Systems Evolution
Department of Evolutionary Genetics
Plön -- GERMANY

§ Institute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE
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