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

Hilmar Lapp hlapp at gmx.net
Sun Jun 25 15:42:20 EDT 2006

We did not and will not deposit 1.5.1 into CPAN due to the API issues  
in some (rather central) interfaces. These issues are changes over  
the 1.4 API and some of those changes are going to go away. Once we  
deposit it into CPAN we would sanction the changed API as the new  
'official' API and would open a huge can of backward liability worms.  
If you just continue to use the 1.4 API on the 1.5.1 release you  
don't need to be concerned about an API method you're using going away.

As I said, the people from the core group of developers who have  
traditionally shepherded releases all think that doing a 1.4.1  
release wouldn't be the best investment of their time. You are most  
welcome to disagree and volunteer your time to coordinate the 1.4.1  
release, and a lot of people will appreciate your efforts - including  
the bioperl developers and 'core'. It shouldn't be much work  


On Jun 25, 2006, at 3:02 PM, Phillip SanMiguel wrote:

> 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
> listening...)
>    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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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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