2011/11/4 Hervé Pagès > 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 > [[alternative HTML version deleted]]