Perhaps a patch to R such that generics don't clobber each-other's method
tables if the signatures agree? I haven't dug deeply, but simply merging
the method tables seems like it would be safe when there are no conflicts.
That way this type of multiplicity would not be a problem, though it
wouldn't help (as it shouldn't) if the two generics didn't agree on
signature or both carried methods for the same class signature.
~G
On Wed, Mar 26, 2014 at 4:38 AM, Michael Lawrence <lawrence.mich...@gene.com
> wrote:
> The BiocGenerics package was designed to solve this issue within
> Bioconductor. It wouldn't be the worst thing in the world to depend on the
> simple BiocGenerics package for now, but ideally the base generics would be
> defined higher up, perhaps in the methods package itself. Maybe someone
> else has a more creative solution, but any sort of conditional/dynamic
> approach would probably be too problematic in comparison.
>
> Michael
>
>
>
> On Wed, Mar 26, 2014 at 4:26 AM, Ulrich Bodenhofer <
> bodenho...@bioinf.jku.at
> > wrote:
>
> > [cross-posted to R-devel and bioc-devel]
> >
> > Hi,
> >
> > I am trying to implement a 'sort' method in one of the CRAN packages I am
> > maintaining ('apcluster'). I started with using setMethod("sort", ...) in
> > my package, which worked fine. Since many users of my package are from
> the
> > bioinformatics field, I want to ensure that my package works smoothly
> with
> > Bioconductor. The problem is that the BiocGenerics package also redefines
> > 'sort' as an S4 generic. If I load BiocGenerics before my package,
> > everything is fine. If I load BiocGeneric after I have loaded my package,
> > my setMethod("sort", ...) is overridden by BiocGenerics and does not work
> > anymore. A simple solution would be to import BiocGenerics in my package,
> > but I do not want this, since many of this package's users are outside
> the
> > bioinformatics domain. Moreover, I am reluctant to include a dependency
> to
> > a Bioconductor package in a CRAN package. I thought that maybe I could
> > protect my setMethod("sort", ...) from being overridden by BiocGeneric by
> > sealed=TRUE, but that did not work either. Any ideas are gratefully
> > appreciated!
> >
> > Thanks a lot,
> > Ulrich
> >
> >
> > ------------------------------------------------------------------------
> > *Dr. Ulrich Bodenhofer*
> > Associate Professor
> > Institute of Bioinformatics
> >
> > *Johannes Kepler University*
> > Altenberger Str. 69
> > 4040 Linz, Austria
> >
> > Tel. +43 732 2468 4526
> > Fax +43 732 2468 4539
> > bodenho...@bioinf.jku.at <mailto:bodenho...@bioinf.jku.at>
> > http://www.bioinf.jku.at/ <http://www.bioinf.jku.at>
> >
> > ______________________________________________
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
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>
--
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis
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