R devel - Mar 2014 - Conflicting definitions for function redefined as S4 generics

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

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>
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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