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

[olivier sallou]

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).

Olivier


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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