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

[Olivier Sallou]

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 <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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>

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

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