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[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>

Thread (8 messages)

Zhilong Jia issue about S4 slot has a dist object. Apr 1 Michael Lawrence issue about S4 slot has a dist object. Apr 1 Hervé Pagès issue about S4 slot has a dist object. Apr 1 Martin Morgan issue about S4 slot has a dist object. Apr 1 Michael Lawrence issue about S4 slot has a dist object. Apr 1 Hervé Pagès issue about S4 slot has a dist object. Apr 1 Michael Lawrence issue about S4 slot has a dist object. Apr 1 Michael Lawrence issue about S4 slot has a dist object. Apr 2