[Bioperl-l] Significant blocker for 1.6.1 : Nexml

[Hilmar Lapp]

I'd suspect that the latest Bio::Phylo changes have been due for CPAN  
release anyway, so unless those are unstable that seems like the  
easiest fix to me.

If the Nexml code works against not yet stable updates to Bio::Phylo,  
it shouldn't be in a BioPerl stable release, right?

	-hilmar

On Sep 8, 2009, at 12:23 AM, Chris Fields wrote:

> All,
>
> I'm running into a pretty significant blocker for 1.6.1 re: Chase's  
> Nexml code.  In particular, I have tried three versions of  
> Bio::Phylo; the default CPAN installation (1.6), the latest CPAN RC  
> (1.7_RC9, not installed by default), and the latest from Bio::Phylo  
> svn:
>
> https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/perl
>
> At this moment only the Bio::Phylo code from svn is working with  
> BioPerl's Nexml modules.  From my local tests Bio::Phylo 1.6 appears  
> to be missing Bio::Phylo::Factory (all Nexml tests fail), whereas  
> 1.7_RC9 has some kind of versioning issue (again, all tests fail).   
> The problem: CPAN will always install 1.6 (the others are RC, so  
> they won't be installed unless the full path is used).  Even so,  
> nothing on CPAN even works; one must use the latest Bio::Phylo SVN  
> code.
>
> ATM I'm just not seeing how this can be released with 1.6.1 right  
> now, unless one of the following occurs:
>
> 1) Rutger V. drops a quick non-RC release to CPAN,
> 2) check for the minimal working Bio::Phylo version and safely skip  
> any Nexml-related tests unless proper version is present (not easy  
> with a $VERSION like '1.7_RC9'),
> 3) push Nexml into it's own distribution (something we were planning  
> on anyway with a number of modules)
>
> As for #3 above, I think it probably belongs in a larger bioperl- 
> phylo as Mark had previously proposed.  I'm open to just about any  
> solution.
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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