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 <zhilong...@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> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel