[Bioc-devel] ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position?

[Michael Love]

thanks for the heads up Lorena and Martin

I've just checked in a DESeq2 using importFrom of ggplot2 functions

I now just have one warning for DESeq2 CHECK:

Warning: multiple methods tables found for ‘relistToClass’

On Sat, Dec 19, 2015 at 2:02 PM, Morgan, Martin <
Martin.Morgan at roswellpark.org> wrote:

> You are right that BiocGenerics creates and exports a generic Position.
>
> I think you are right that the warning is coming from DESeq2, which
> imports(BiocGenerics) and imports(ggplot2).
>
> The solution is for the DESeq2 author to do as you did, importFrom()
> selectively, or continue to declare Imports: in the DESCRIPTION file but
> use ggplot2::Position, etc., in the R code.
>
> I am confident that this will be cleaned up by the DESeq2 author in the
> near future; there are a number of other problems likely to be introduced
> by ggplot2 changes in other Bioconductor packages.
>
> Martin
>
> ________________________________________
> From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Lo [
> lorena.pantano at gmail.com]
> Sent: Saturday, December 19, 2015 12:35 PM
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] ggplot2 2.0.0 export Position now, conflict with
> BiocGeneric::Position?
>
> Hi all,
>
> maybe this is so stupid, I just updated to R 3.3 and all packages,
> including gglot2 (2.0.0, two days ago).
>
> I noticed ggplot2 now export Positions, and I think BiocGenerics as well
> has that?
>
> Now I having problems with my package that is under review in the
> package builder with this warning:
>
> Warning: replacing previous import by ‘ggplot2::Position’ when loading
> ‘DESeq2’
>
> I import DESeq2 and DESeq2 import ggplot2. I was importing as well
> ggplot2, so I was seeing this warning twice. I had to use importFrom to
> fix it. Now I only see the warnings once.
>
> Could someone try to replicate?
>
> I just updated ggplot2 to 2.0.0 in R3.3 and installed devel version of
> DESeq2, and I get the warning. I guess any package importing ggplot2
> should do the same.
>
> I just want to know if it is some stupid thing I am doing, or this will
> start happening always n the future?
>
> sorry if it was stupid.
>
> thanks
>
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