On Mon, May 17, 2010 at 10:49 AM, Mike Dewar <mike.dewar@columbia.edu>wrote:

> Hello,
>
> I asked a question last week about how to submit patches.
>
> After hacking on the code ('annotationTools') for a while I realised (
> http://biostar.stackexchange.com/questions/1054/homology-bioconductor)
> that it was either the wrong package for the job or, what I think is more
> likely, a package that had been largely superseded by another package
> ('biomaRt').
>
> So I have a new question, or maybe it's a suggestion: is there a way to
> mark packages for removal, or to add something to their entry in
> bioconductor that says "this package has been largely replaced by this other
> package"?
>

We do remove packages.  When package functionalities decay, R supports a
Deprecated/Defunct annotation/user redirection process, and this is used in
Bioconductor when appropriate.


>
> I should say that I feel rather mean asking this question, and it shouldn't
> reflect badly on the authors of the package in question. It's just had their
> been a pointer on the annotationTools package that said "these days, you
> should maybe check out 'biomaRt'" I would have saved myself quite a lot of
> time. And I guess, in such a rapidly evolving area, and with such a large
> code base, this sort of thing will be required sooner or later?
>
>
Your judgment on the duplication of annotationTools functionality by biomaRt
seems to me overbroad.  The annotationTools vignette shows various
functionalities that are not supported by biomaRt.   I see no reason that
the two should not coexist.

Cheers,
>
> Mike Dewar
>
> On 13 May 2010, at 12:26, Vincent Carey wrote:
>
> The short answer is 'no', nothing official.  The long answer is that
> dealing with such improvements is up to the maintainer of the specific
> package affected.  If the maintainer is identified in the package
> DESCRIPTION, contact him/her directly.  If you don't see a maintainer
> identified (bioconductor devel team, for example, is listed as the package
> maintainer) you could contact any of the developers directly.  For example,
> you could write to me.
>
> On Wed, May 12, 2010 at 12:39 PM, Mike Dewar <mike.dewar@columbia.edu>wrote:
>
>> Hello,
>>
>> If I make some improvements to a piece of code included in Bioconductor,
>> is there an 'official' way of submitting the improvements for future
>> inclusion?
>>
>> Cheers,
>>
>> Mike Dewar
>>
>>
>> - - -
>> Dr Michael Dewar
>> Postdoctoral Research Scientist
>> Applied Mathematics
>> Columbia University
>> http://www.columbia.edu/~md2954/ <http://www.columbia.edu/%7Emd2954/>
>>
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>>
>
>
> - - -
> Dr Michael Dewar
> **Postdoctoral Research Scientist
> Applied Mathematics
> Columbia University
> http://www.columbia.edu/~md2954/ <http://www.columbia.edu/%7Emd2954/>
>
>
>
>
>
>
>

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