[Bioc-devel] Package warning due to function replacement

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Fri Sep 23 15:13:14 CEST 2016

In general you can assume this to be the case for core functionality like
the stuff in Biobase.

What you should do however, since combine() is an S4 method, is import the
S4 method from BiocGenerics.  In fact, it is a good idea to check which
generics are defined in BiocGenerics and consider whether your package
  - support a method for some of these generics (probably not all of these
methods, just the few that might make sense; this is very package dependent)
  - import them

In my own work I just do


On Fri, Sep 23, 2016 at 7:59 AM, THEVENOT Etienne 207099 <
Etienne.THEVENOT at cea.fr> wrote:

> Dear Bioc Team,
> First of all thanks a lot again for all the time you spend developing and
> maintaining the Bioc repository.
> I recently added 'Biobase' as "suggests" in the 'biosigner' package in
> order to have the biosign method work on 'ExpressionSet' objects (devel
> version of 'biosigner').
> Since it appears that the 'combine' method from 'Biobase' is common to a
> combine method from 'randomForest' (imported in 'biosigner'), the following
> warning is generated:
> Warning: replacing previous import 'Biobase::combine' by
> 'randomForest::combine' when loading 'biosigner'
> This message is fine for me (the 'combine' method from Biobase is not used
> in 'biosigner'), but I wanted to check that getting such a warning will not
> prevent the devel version to move into the next bioc release.
> I thank you in advance for your answer.
> Kind Regards,
> Etienne.
>         [[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list