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 <ti...@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 > -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
