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

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

Re: [Bioc-devel] [Rd] For integer vectors, `as(x, "numeric")` has no effect.

As I tried to say on Dec. 11, there are two levels of "fix": 1. The fix to the complaint in the OP's subject heading is to conform to the default third argument, strict=TRUE: as(1L, "numeric") == 1.0 This generates some incompatibilities, as for classes that extend "numeric". But still leaves

[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

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

Also for what it's worth the most recent R-devel reports more informatively: 4: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'DESeq2' Thanks to this commit: ~/src/R-devel$ svn log -r69783

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

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 <

Re: [Bioc-devel] [Rd] For integer vectors, `as(x, "numeric")` has no effect.

> Martin Maechler > on Sat, 12 Dec 2015 10:32:51 +0100 writes: > John Chambers > on Fri, 11 Dec 2015 10:11:05 -0800 writes: >> Somehow, the most obvious fixes are always back-incompatible these days. >> The example