2011/11/4 Hervé Pagès <hpages@fhcrc.org>

> Hi Steve,
>
>
> On 11-11-04 02:02 PM, Steve Lianoglou wrote:
>
>> Hi all,
>>
>> It looks like the `genome` generic function from rtracklayer has moved
>> to GenomicRanges in the 2.9 release train, and subsequently lost its
>> `...` param.
>>
>
> I moved it, together with the `genome<-` generic, and dropped the `...`
> arg from `genome` because (1) I couldn't find any method in BioC
> that uses this arg, (2) `genome` (getter) and `genome<-` (setter)
> are aimed to be accessors and it's unusual to have `...` in an
> accessor, (3) it was a little bit ackward to have `...` in the getter
> but not in the setter.
>
>
>
>> Would anybody mind if I add the `...` back to the genome function now
>> defined in GenomicRanges? I'll be careful to update the setMethods
>> where appropriate in GenomicRanges, but I guess other packages will
>> also need to update (rtracklayer) that I can't commit to.
>>
>
> In devel? Sure. It's a perfect time to break things ;-) I'm not so sure
> about release though. What other people think?
>
>
>
Do we really need to modify every method? I think changing the generic is
all that is really necessary.


>
>> I was `importFrom(rtracklayer, genome)`-ing the genome function in one
>> of my packages ... switching it to importFrom GenomicRanges isn't a
>> problem, but I use the `...`
>>
>> (here's another post that touches on the "need" for a centralized
>> BiocGenerics (or whatever) package that pops up from time to time).
>>
>
> Not every generic is going to make it to BiocGenerics. Also a generic
> function is not just a name, there are also some expectations about what
> kind of operation its methods should do.
>
> Cheers,
> H.
>
>
>> Thanks,
>> -steve
>>
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
> ______________________________**_________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/**listinfo/bioc-devel<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>

	[[alternative HTML version deleted]]

