Re: [Rd] [Bioc-devel] Conflicting definitions for function redefined as S4 generics

2014-04-03 Thread Michael Lawrence
On Thu, Apr 3, 2014 at 4:33 AM, Ulrich Bodenhofer wrote: > On 03/27/2014 06:31 PM, Hervé Pagès wrote: > >> On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote: >> >>> [...] >>> >>> >>> For the time being, it seems I have three options: >>> >>> 1) not supplying the sort() function yet (it is not yet in

Re: [Rd] [Bioc-devel] Conflicting definitions for function redefined as S4 generics

2014-04-03 Thread Ulrich Bodenhofer
On 03/27/2014 06:31 PM, Hervé Pagès wrote: On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote: [...] For the time being, it seems I have three options: 1) not supplying the sort() function yet (it is not yet in the release, but only in my internal devel version) 2) including a dependency to BiocG

Re: [Rd] [Bioc-devel] Conflicting definitions for function redefined as S4 generics

2014-03-27 Thread Hervé Pagès
On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote: I fully agree, Michael, that this would be a great thing to have! I have often wondered why R and the standard packages are still sticking so much to the old-style S3 flavor though S4 is part of standard R. I acknowledge that backward compatibili

Re: [Rd] [Bioc-devel] Conflicting definitions for function redefined as S4 generics

2014-03-26 Thread Hervé Pagès
Hi, I agree. I can't think of an easy way to avoid this kind of clashes between BioC and non-BioC S4 generics, other than by having things like sort() already defined as an S4 generic in base R. Note that, just having setMethod("sort", ...) in your package Ulrich, and not putting a setGeneric()