[Bioperl-l] BioPerl 1.6 RC1

Chris Fields cjfields at illinois.edu
Fri Jan 2 10:27:55 EST 2009

On Dec 26, 2008, at 4:07 PM, Sendu Bala wrote:

> Alex Lancaster wrote:
>> Some other oddness: when the Build.PL script checks for the
>> dependencies, it notes a few optional CPAN packages which aren't yet
>> packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random',
>> are missing.  Since they are optional and missing dependencies, I
>> would have expected that the relevant bioperl modules such
>> Bio::PhyloNetwork should also not be installed, but it appears that
>> the .pm files are installed, see lines like:
>> Copying Bio/PhyloNetwork/Factory.pm -> blib/lib/Bio/PhyloNetwork/ 
>> Factory.pm
>> from the full build.log:
>> https://koji.fedoraproject.org/koji/getfile?taskID=1022511&name=build.log
>> This causes problems because RPM then generates Requires such as:
>> Requires: perl(Algorithm::Munkres)
>> (see bottom of the build.log referred to above) which can't (yet) be
>> fullfilled by any other package in the Fedora package set, leading to
>> broken dependencies.
>> Is this the expected behaviour upon missing optional dependencies?
> Yes, though I can see how it's broken from your point of view. It is  
> set up to install everything, but simply not everything will work  
> without the optionals. I hadn't considered not installing the  
> modules that won't work.
> Something to think about, but it's probably not going to happen for  
> 1.6?

Not for 1.6.0, maybe for 1.6.x.  This would need to be worked out on  
main trunk and merged over to the branch if it works.


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