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

Guest, Simon Simon.Guest at agresearch.co.nz
Mon Apr 30 02:00:26 EDT 2012


Dear BioPerlers,

I am building BioPerl and BioPerl-Run as RPMs, since I have to install them on
several servers, and really don't want to run CPAN installation scripts on
each machine.

It has been a tortuous journey of chasing down dependencies and packaging them
(thank goodness for cpanspec), but I think I am nearly done.

However, I have hit a circular dependency / incompatibility problem between
BioPerl and BioPerl-Run.

When building BioPerl-Run-1.006900, it insists on BioPerl-1.6.901:
Checking prerequisites...
- ERROR: Bio::Root::Version (1.006001) is installed, but we need version >= 1.006900

But then BioPerl-Run-1.006900 has dependencies on
    Bio::Expression::DataSet
    Bio::Expression::Platform
    Bio::Expression::Sample
    Bio::Expression::Contact
which seem to be in BioPerl-1.6.1 but not BioPerl-1.6.901

Does anyone know of this problem?

Are there any suggestions for work arounds?

cheers,
Simon

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