[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 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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