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

[Zhilong Jia]

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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