[Bioc-devel] issue about S4 slot has a dist object.

Michael Lawrence lawrence.michael at gene.com
Thu Apr 2 00:28:52 CEST 2015

Using setOldClass is generally fine. In this case, the graph package is
already defining the dist class, so you could just import that. The graph
package might have to export it though.

On Wed, Apr 1, 2015 at 3:15 PM, Zhilong Jia <zhilongjia at gmail.com> wrote:

> Hi,
> Here is the package. (https://tracker.bioconductor.org/issue1204 or
> https://github.com/zhilongjia/cogena; ). When I biocCheck it, there is a
> note.
> Note: the specification for S3 class “dist” in package ‘cogena’ seems
> equivalent to one from package ‘graph’: not turning on duplicate class
> definitions for this class.
> In the source code, there are two R files are related with this issue,
> cogena_class.R
> and  <https://github.com/zhilongjia/cogena/blob/master/R/cogena_class.R>
> dist_class.R
> <https://github.com/zhilongjia/cogena/blob/master/R/dist_class.R> in the R
> dir. Here there is a dist slot in cogena class. In the dist_class.R
> <https://github.com/zhilongjia/cogena/blob/master/R/dist_class.R>, I use
> setOldClass, but it seems it is not recommended by Bioconductor.
> How to repair this issue? Thank you.
> Regards,
> Zhilong
> <https://github.com/zhilongjia/cogena/blob/master/R/cogena_class.R>
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