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.mor...@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-boun...@r-project.org] on behalf of Lo [ > lorena.pant...@gmail.com] > Sent: Saturday, December 19, 2015 12:35 PM > To: bioc-devel@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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel