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

Phillip SanMiguel pmiguel at purdue.edu
Sat Jun 24 15:37:08 EDT 2006


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?

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?

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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