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

[Morgan, Martin]

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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