[Bioc-devel] Package warning due to function replacement

[Kasper Daniel Hansen]

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
should
  - 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
  import(BiocGenerics)
in the NAMESPACE.

Best,
Kasper

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.
>
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