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

Hilmar Lapp hlapp at gmx.net
Sat Jun 24 21:02:36 EDT 2006

On Jun 24, 2006, at 3:37 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  
> 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?

Either way. If the patch is trivial you could also provide the patch  
as an option. Generally we don't support that though. (Not everything  
that we don't support we don't support because it doesn't work.  
Sometimes it's just a statement along 'it-probably-works-but-don't- 

> 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?

1.5.1 fixes a number of other problems too, so there isn't really  
much reason to upgrade to 1.4.1 if there was one instead of to 1.5.1,  
so investing time into creating 1.4.1 we think is not the best  
investment we can make.

Our current goal is to release 1.5.2 and possibly more development  
versions all leading on a steady path to 1.6.0. There's very few (but  
significant) stumbling blocks on this path that will require I  
believe some dedicated time from a couple  of people and after that  
there shouldn't be any real obstacles. It's quite possible that at  
BOSC or as early as next week at the GMOD meeting we could see a leap  
forward, typically it's those meetings that pull the respective  
people away from their daily obligations (short of an actual  

Some time back in spring 1.6 was put in proximity to BOSC, but that's  
probably not going to happen, but quite possibly not that much  


> 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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> Bioperl-l at lists.open-bio.org
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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