[Bioperl-l] How to handle bugs in bioperl 1.4 on CPAN?

[Chris Fields]

On Jun 24, 2006, at 2:37 PM, Phillip SanMiguel wrote:

> Here is an example bug:
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=1682
>
> It was a bug fixed in a module in BioPerl 1.4  back in October of  
> 2004.
> The module was Bio::Seq::QualI.  The patch resulted in v. 1.7 of the
> module. However the version of the module currently available from  
> CPAN
> is 1.6. (That is the current "stable" release, BioPerl 1.4.0)
>
> I've written a script that relies on that bug being fixed. How  
> should I
> deal with this when I want to give the script to others to use? Just
> tell them "You must have BioPerl 1.5 installed". Give them  
> instructions
> for patching the module code?

A BioPerl module version is not the same as the distribution  
version.  All the modules have different version numbers  
corresponding to CVS commits for various code changes.  If you want  
to see the version for the distribution, read this:

http://www.bioperl.org/wiki/ 
FAQ#How_can_I_tell_what_version_of_BioPerl_is_installed.3F

Many 'bug fixes', you'll find, have less to do with problems/bugs in  
BioPerl code than they do with outside code changes beyond our  
control.  By that I mean changes to other programs modify output so  
parsers break (BLAST, PAML, etc), or changes to API for remote  
databases that break queries (recent changes in EBI database  
concerning Swissprot, for example).  So, the code is considered  
'stable' at the time of release, but past that point issues beyond  
our control may break certain modules parsing output, accessing  
remote databases, and so on, at any time. This link:

http://www.bioperl.org/wiki/FAQ#BioPerl_in_General

should answer a few more questions you may have.  The FAQ is very  
helpful...

In general, if there are problems with code you could look at the  
latest developer's release (1.5.1, released in Oct 2005) to see if  
any bugs have been fixed.  They may be fixed post-1.5.1 and will be  
in CVS; you can always suggest using 1.5.1 (it's pretty stable) and  
updating only the fixed modules from CVS if needed.

> How long before the next "stable" release? Maybe a year? Should not a
> BioPerl 1.4.1 be released so CPAN would get bug fixes like this  
> one? Or
> would that be very difficult?

No, it's not that easy.  BioPerl isn't like most CPAN modules with  
one or two developers.  See the wiki page for details on planning  
releases to see why:

http://www.bioperl.org/wiki/Making_a_BioPerl_release

It takes a lot of effort and coordination, much more so than the  
average CPAN module.  I believe some of the core developers are  
meeting this weekend; maybe something will come of that and we'll get  
an idea of a next release.

Chris

> By the way, I think the revision graph viewer is great for someone, at
> best, peripherally involved in BioPerl to figure out which module
> version is associated with which BioPerl version, for example:
>
> http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/Bio/Seq/ 
> QualI.pm?graph=1
> Phillip SanMiguel
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign