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

Chris Fields cjfields at uiuc.edu
Sat Jun 24 21:40:49 EDT 2006

> > 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-
> bug-us-if-it-doesn't'.)

The bug was fixed post-1.4 release according to the link, so Phillip should
use v1.5.1 or newer.

Hilmar's right.  It's hard to address every single complaint about code not
working or method not implemented w/o having patches or fixes submitted.
It's not my top priority to fix bugs in modules submitted by other authors
when I don't know the code.  I'll try if I have the free time, but that's
getting to be a precious commodity lately...

> > 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
> hackathons).
> 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
> afterwards.
> 	-hilmar

Nice to know.  I guess a Release Pumpkin will be picked as well.  BOSC is
right around the corner so I guess we can expect something announced soon as
to a possible roadmap (we can't talk about 'timelines' in the States, it's
not patriotic).  


More information about the Bioperl-l mailing list