[Rd] Conflicting definitions for function redefined as S4 generics

Ulrich Bodenhofer bodenhofer at bioinf.jku.at
Wed Mar 26 12:26:16 CET 2014

[cross-posted to R-devel and bioc-devel]


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,

*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>

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