[Bioperl-l] BioPerl 1.6 RC1

Hilmar Lapp hlapp at gmx.net
Fri Dec 26 19:15:22 EST 2008

On Dec 26, 2008, at 4:39 PM, Alex Lancaster wrote:

> 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

I may have failed to chime in here earlier at the appropriate  
opportunity, but I would be very hesitant about putting  
Bio::PhyloNetwork into the stable release.

These modules have never been announced or discussed on the mailing  
list with other developers AFAIAA, and so have never received any  
scrutiny. I'm also not sure who else other than the authors are using  
them, so I don't think there's a user base yet that could substitute  
for developer scrutiny. One simple suggestion for example would be to  
move them into Bio::Phylo::Network, so as not to unnecessarily  
proliferate the first level package directory. So at the very least it  
should be obvious to anyone that the API including the module names  
are subject to change.


: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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