[Bioc-devel] R6 and Bioconductor

Martin Morgan martin.morgan at roswellpark.org
Fri May 12 13:11:24 CEST 2017

On 05/12/2017 02:05 AM, Garth Ilsley wrote:
> Hello,
> I am thinking of creating package for Bioconductor, and I am wondering about the use of R6 classes (from the R6 package). I do indeed intend to use existing Bioconductor classes such as SummarizedExperiment and interact and make use of other Bioconductor packages, such as scater and DESeq2. This appears to be in accordance with the guidelines (https://www.bioconductor.org/developers/package-guidelines/#classes), but does the use of R6 classes disqualify the package from being in Bioconductor? Do I need to write my classes as S4 in order to qualify?

I think there's little value in exposing R6 classes to Bioconductor 
users, introducing yet another syntax and semantics, and would strongly 
discourage their use outside the package name space.

Inside the package name space the maintainer has more liberty to adopt 
programming practices that are geared toward correct and efficient 
implementations; if R6 fills this role (I'm not an expert, but I don't 
think R6 enforces strong type checking and is not particularly 
efficient) then it would be appropriate to use them.


> Thank you for your help.
> Best regards,
> Garth
> 	[[alternative HTML version deleted]]
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