From bodenhofer at bioinf.jku.at  Thu Apr  3 13:33:23 2014
From: bodenhofer at bioinf.jku.at (Ulrich Bodenhofer)
Date: Thu, 03 Apr 2014 13:33:23 +0200
Subject: [Rd] [Bioc-devel] Conflicting definitions for function
 redefined as S4 generics
In-Reply-To: <5334605D.5080809@fhcrc.org>
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	<5333EBBB.80007@bioinf.jku.at> <5334605D.5080809@fhcrc.org>
Message-ID: <533D4703.8070705@bioinf.jku.at>

On 03/27/2014 06:31 PM, Herv? Pag?s 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 BiocGenerics
>> 3) leaving the problem open, mentioning in the documentation that users
>> who want to use apcluster in conjunction with Bioconductor should load
>> BiocGenerics first
>
> 4) define an S3 method, as mentioned in my previous post
>
> H.
>
After a while, I came back to this suggestion. Thanks, Herv?! I now 
tried it and it indeed works smoothly: all problems I mentioned - as you 
expected correctly - are resolved. It seems that BiocGenerics screws up 
my previously defined S4 generic, but leaves my S3 function untouched. 
Hmm ...

The question is whether it is good style to use S3 and S4 together. 
Actually I am reluctant to think so, but if it helps and creates no 
other problems whatsoever, why not?

Cheers,
Ulrich



[Rd] [Bioc-devel] Conflicting definitions for function redefined as S4 generics
Ulrich Bodenhofer