[Bioperl-l] Significant blocker for 1.6.1 : Nexml

[Chris Fields]

On Sep 8, 2009, at 7:16 AM, Hilmar Lapp wrote:

> 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.

My thought as well, just not sure how stable that code is right now.   
Bio::Phylo has been in RC for a while now, correct?

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

Right.  That should be sorted out first.

I can wait a bit longer for Rutger to respond; there are a few other  
odds and ends that can been worked on in the meantime.  I would like  
to get the alpha out soon and 1.6.1 in the next week or so though.

chris

> 	-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 :
> ===========================================================
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l