[Bioperl-l] bioperl 1.6

Chris Fields cjfields at uiuc.edu
Thu Jul 31 16:01:02 EDT 2008

On Jul 31, 2008, at 9:37 AM, Brian Osborne wrote:

> Chris,
> Yes, I volunteered to look at these, and I did take a look. What's  
> not clear to me though is if BioRuby is saying these issues are  
> "nice to fix" but insubstantial or if they are truly important.
> I'd hesitate to call these a block to releasing 1.6 if they don't  
> block the use of OBDA, and I have no idea if these "block" anyone  
> over at BioRuby or not. To my knowledge these bugs don't appear when  
> one uses OBDA with Bioperl.
> Specifically, it would be nice to see the code where these bugs show  
> themselves.
> Brian O.


I agree that these don't block the use of OBDA within BioPerl.    
However I'm worried they possibly block cross-language OBDA use, for  
instance if one built the flatfile database in BioPerl and used OBDA- 
specific flatfile adaptors for BioRuby (and possibly vice versa).

I think the bug submitter indicated conflicts with OBDA  
specifications, though you commented about these issues already in the  
bug reports.  I suspect you (and others involved with OBDA)` can more  
readily identify whether the bug is ours or in BioRuby code, so this  
is something we should bring up with the BioRuby folks.  Regardless,  
any bioperl-specific fixes related to this can be included in a later  
point release on the 1.6 branch.


PS: for those following, the specific bugs are 2336-2339 in bugzilla,  
and specifically flatfiles via Bio::DB::Flat.

More information about the Bioperl-l mailing list