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

Fields, Christopher J cjfields at illinois.edu
Mon Apr 30 09:42:34 EDT 2012


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.

chris

On Apr 30, 2012, at 1:00 AM, Guest, Simon wrote:

> 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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