On 07/31/2013 04:19 PM, Andreas Tille wrote: > 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. I suspect upstream did this to avoid needing complete bioperl dependency. > > Kind regards > > Andreas. > >> 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 >> _______________________________________________ >> Debian-med-packaging mailing list >> debian-med-packag...@lists.alioth.debian.org >> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging >
-- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
