Message-ID: <CACQE_YyRG0OA9s2mEc9X6qXn=vx-=h4Rg7sPdBVzzcOkr5VSCg@mail.gmail.com>
Date: 2015-04-01T22:15:45Z
From: Zhilong Jia
Subject: [Bioc-devel] issue about S4 slot has a dist object.
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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