[Bioperl-l] Circular dependency problems packaging BioPerl as RPM

Guest, Simon Simon.Guest at agresearch.co.nz
Mon Apr 30 23:29:58 EDT 2012

> -----Original Message-----
> From: Fields, Christopher J [mailto:cjfields at illinois.edu]
> Sent: Tuesday, 1 May 2012 1:43 a.m.
> To: Guest, Simon
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Circular dependency problems packaging BioPerl as
> The Bio::Expression dependencies are unusual, I'll have to look through and
> find the modules responsible for pulling these in.  When I last ran these no
> tests failed, so either the dependency is off or no tests have been written for
> the modules in question.
> We can always release a new CPAN BioPerl-Run to deal with it.

Hi Chris,

I ignored the Bio::Expression dependencies and everything eventually built OK, using BioPerl-1.6.901 and  BioPerl-Run-1.006900.

If you release a new BioPerl-Run, I would be interested in packaging it, as I have come this far.

Do you have any ideas about where I could submit the BioPerl and dependency RPMs I built for CentOS 6?  I now have around 40 RPMs that weren't in CentOS or EPEL, which were all built straight from CPAN using cpanspec.  I guess others might like to benefit from this (and it would also serve to validate the builds).

My other unknown is what non-Perl dependencies I should add to the BioPerl RPM.  I don't know what to do here.  The dependencies page on the BioPerl Wiki seems to list only Perl module dependencies.


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