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] ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position?
4 messages · Lorena Pantano, Martin Morgan, Michael Love
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?
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 _______________________________________________ Bioc-devel at 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.
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-bounces at r-project.org] on behalf of Morgan, Martin [Martin.Morgan at roswellpark.org]
Sent: Saturday, December 19, 2015 2:02 PM
To: Lo; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position?
Sent: Saturday, December 19, 2015 2:02 PM
To: Lo; bioc-devel at 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-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 _______________________________________________ Bioc-devel at 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 at 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.
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 _______________________________________________ Bioc-devel at 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.