[Bioperl-l] removing BioPerl 1.x from CPAN ?

Thu Jan 20 21:13:30 UTC 2011

No, only the older (out-of-date) versions of BioPerl-related code itself would be removed.  Any other Bio::* modules in any other distribution wouldn't be touched (actually, couldn't be touched, unless they were removed by the distribution author).

Dave, we may need to contact Sendu as well, noticed he has the 1.5.2 developer releases on CPAN as well:

http://search.cpan.org/~sendu/

chris

On Jan 20, 2011, at 2:43 PM, Tom Keller wrote:

> Would the entire Bio directory disappear?
> How would one get modules that are not part of bioperl-live or the other main packages?
> (for example Bio::Trace::ABIF)
> 
> thanks,
> Tom
> MMI DNA Services Core Facility
> 503-494-2442
> kellert at ohsu.edu
> Office: 6588 RJH (CROET/BasicScience)
> 
> 
> 
> 
> 
> On Jan 20, 2011, at 9:00 AM, <bioperl-l-request at lists.open-bio.org> <bioperl-l-request at lists.open-bio.org> wrote:
> 
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>> Today's Topics:
>> 
>>  1. Re:  Frame translation gets an extra aa? (Karger, Amir)
>>  2.  removing BioPerl 1.x from CPAN ? request for comment
>>     (Dave Messina)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Wed, 19 Jan 2011 12:36:02 -0500
>> From: "Karger, Amir" <akarger at CGR.Harvard.edu>
>> Subject: Re: [Bioperl-l] Frame translation gets an extra aa?
>> To: Chris Fields <cjfields at illinois.edu>
>> Cc: "bioperl-l at lists.open-bio.org" <bioperl-l at lists.open-bio.org>
>> Message-ID:
>> 	<1B12003244CE894E85B472602363788831A884DE at FASXCH01.fasmail.priv>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>>> From: Chris Fields [mailto:cjfields at illinois.edu]
>>> 
>>> I wrote: 
>>>> there should be
>>> some way to do either assuming or not assuming without too much
>>> extra work.... the extra object copying
>>> might be a problem if you were trying to write fast code, which
>>> luckily I'm not in this case.
>>> 
>>> Fast code and BioPerl?  We're trying to make things faster, but
>>> this may be more difficult in practice with the default OO system
>>> (and a complete switch to Moose will be problematic in the short
>>> term).
>>> 
>>> I have committed a fix to github for the above.  Basically, setting
>>> either '-complete' or '-complete_codons' will fill out partial
>>> codons and attempt to translate them, but this behavior is off by
>>> default.  I think this makes sense, just from the perspective we
>>> don't want unintended side-effects.
>> 
>> That makes sense to me. The truth is, there shouldn't be that many real life applications, as far as I can tell, where this bites people meaningfully. But having the option is nice.
>> 
>> -Amir
>> 
>> 
>> 
>> ------------------------------
>> 
>> Message: 2
>> Date: Thu, 20 Jan 2011 17:11:01 +0100
>> From: Dave Messina <David.Messina at sbc.su.se>
>> Subject: [Bioperl-l] removing BioPerl 1.x from CPAN ? request for
>> 	comment
>> To: Dave Messina <David.Messina at sbc.su.se>
>> Message-ID: <F4E417F1-6D80-4C70-ADEE-B25AB291E730 at sbc.su.se>
>> Content-Type: text/plain; charset=us-ascii
>> 
>> Hi everybody,
>> 
>> As some of you have no doubt noticed, we have a persistent problem with users accidentally using BioPerl versions 1.4 and earlier. Although they've been placed on BackPAN, CPAN's archive for deprecated software, for some reason they still show up in CPAN search results.
>> 
>> It's frustrating for users to be directed to the wrong version of the software, adding another gotcha to an already too-complicated installation process. And to this day it generates support emails on this list.
>> 
>> As far as I know, the Ensembl Perl API still designates version 1.2.3 of BioPerl for use with it:
>> 
>> 	http://www.ensembl.org/info/docs/api/api_installation.html
>> 
>> (although in Chris Fields' testing, the Ensembl API worked just fine with the current BioPerl version, 1.6.x.)
>> 
>> 
>> I intend to ask the CPAN admins to remove BioPerl 1.4 and earlier entirely. But before I do, I wanted to raise the issue here in case anyone objects. In particular, it'd be great if someone from Ensembl could weigh in on this. I should also point out that we have these earlier releases archived on github already, so they will still be available.
>> 
>> 
>> Thanks,
>> Dave
>> 
>> 
>> 
>> 
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>> End of Bioperl-l Digest, Vol 93, Issue 16
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