[Debian-med-packaging] Bug#718407: grinder: fails to install, trying to overwrite other packages files: /usr/share/man/man3/Bio::SeqFeature::Primer.3pm.gz

[Andreas Tille]

Hi Olivier,

On Wed, Jul 31, 2013 at 04:12:40PM +0200, olivier sallou wrote:
> I consider this is a BioPerl element, copied in grinder. It should be
> removed from grinder and depend on bioperl (if not already the case).

This is what I suspected as well - but I was wondering whether it might
be compatible with the rest of the perl code of grinder (which Depends
from libbio-perl-perl) and while stripping of the affected files would
come cheap I liked to ask here for other opinions.  If you think it is
safe to do so I could prepare a fix for uploading.

Kind regards

       Andreas.

> 2013/7/31 Andreas Tille <tille at debian.org>
> 
> > Hi Andreas,
> >
> > thanks for your great QA work.
> >
> > On Wed, Jul 31, 2013 at 11:18:48AM +0200, Andreas Beckmann wrote:
> > >   dpkg: error processing /var/cache/apt/archives/grinder_0.5.3-1_all.deb
> > (--unpack):
> > >    trying to overwrite
> > '/usr/share/man/man3/Bio::SeqFeature::Primer.3pm.gz', which is also in
> > package libbio-perl-perl 1.6.901-3
> > >   dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
> > >   Errors were encountered while processing:
> > >    /var/cache/apt/archives/grinder_0.5.3-1_all.deb
> >
> > I've checked what files might be in common and here is a list:
> >
> >
> > bioperl-1.6.901/usr/share/perl5/Bio:
> > DB
> > PrimarySeqI.pm
> > PrimarySeq.pm
> > Seq
> > SeqFeature
> > Tools
> >
> > bioperl-1.6.901/usr/share/perl5/Bio/DB:
> > Fasta.pm
> >
> > bioperl-1.6.901/usr/share/perl5/Bio/Seq:
> > SeqFastaSpeedFactory.pm
> >
> > bioperl-1.6.901/usr/share/perl5/Bio/SeqFeature:
> > Primer.pm
> >
> > bioperl-1.6.901/usr/share/perl5/Bio/Tools:
> > IUPAC.pm
> >
> > ------------------------------------------------
> >
> > grinder-0.5.3/usr/share/perl5/Bio:
> > DB
> > PrimarySeqI.pm
> > PrimarySeq.pm
> > Seq
> > SeqFeature
> > Tools
> >
> > grinder-0.5.3/usr/share/perl5/Bio/DB:
> > Fasta.pm
> >
> > grinder-0.5.3/usr/share/perl5/Bio/Seq:
> > SeqFastaSpeedFactory.pm
> >
> > grinder-0.5.3/usr/share/perl5/Bio/SeqFeature:
> > Primer.pm
> >
> > grinder-0.5.3/usr/share/perl5/Bio/Tools:
> > IUPAC.pm
> >
> >
> >
> > I have also attached a diff
> >
> >    diff -ubrN grinder-0.5.3 bioperl-1.6.901
> >
> > to this mail were you can see the changes of the files that are shiped
> > with grinder compeeting with potentially newer versions of bioperl.  I
> > wonder what bioperl experts might suggest whether we could simply drop
> > the old copies inside Grinder or whether we need to do some other means
> > to fix this problem.  May be we should also contact the authors of
> > Grinder but I'd ask for some internal opinions first.
> >
> > Kind regards
> >
> >        Andreas.
> >
> > --
> > http://fam-tille.de
> >
> 
> 
> 
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