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 <bodenhofer@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
> bodenhofer@bioinf.jku.at <mailto:bodenhofer@bioinf.jku.at>
> http://www.bioinf.jku.at/ <http://www.bioinf.jku.at>
>
> ______________________________________________
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>

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