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

Phillip SanMiguel pmiguel at purdue.edu
Sun Jun 25 15:02:14 EDT 2006

Chris Fields wrote:
> On Jun 24, 2006, at 2:37 PM, Phillip SanMiguel wrote:
> [...]
>> 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
Hi Chris,
   Thanks for the information--the key part being that a bug fix from a 
couple of years ago has not propagated into the current stable release. 
Below I'll try to convince you that this is a serious problem. (Not 
because it is your fault, of course. I'm just trying to deliver my take 
on the situation to the bioperl-programmer-warriors who happen to be 
   It isn't a problem for me to edit the offending statement in the 
QualI.pm module on systems I generally use. Or even install a 
developer's release of bioperl. My problem is one of advocacy. Maybe I 
have a warped view of the world, but it seems that except for those 
directly involved in the bioperl or GMOD projects, everyone looks to 
CPAN when they install bioperl.
    I write scripts that I sometimes want to send to biologists even 
less programming-capable than I am. I can just barely envision those 
biologists pestering their sysadmin to do a CPAN install of bioperl 
modules so that my script will work. But installing a non-CPAN set of 
modules probably isn't going to happen.
    So, this being the case, how can I, with a clear conscious, advocate 
bioperl to the junior bioinformaticians with whom I happen to interact?
    My take, for what it is worth, is that 1.5 has become an unratified 
stable release. How hard would it be to take 1.5.1--as is--and deposit 
that in CPAN? What would be the downside?

Phillip SanMiguel

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