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 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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[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
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 r69783 | ripley | 2015-12-19 03:24:12 -0500 (Sat, 19 Dec 2015) | 1 line do not report identical re-imports otherwise report where they are from Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Morgan, Martin [martin.mor...@roswellpark.org] Sent: Saturday, December 19, 2015 2:02 PM To: Lo; bioc-devel@r-project.org Subject: 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 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. ___ 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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 < 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
