Can you be more specific about which docker image you pulled? Dan
----- Original Message ----- > From: "Federico Marini" <mari...@uni-mainz.de> > To: "Martin Morgan" <martin.mor...@roswellpark.org>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Thursday, March 3, 2016 1:20:46 AM > Subject: Re: [Bioc-devel] Imports, depends and warnings > You're right, sorry for the misunderstanding. > By updating to a more recent R devel the warning disappears. I probably > should do it more often for development sakes ... > > Side question but related to this, shouldn't the R version in the > current docker container for devel_* be the R devel? On the one I pulled > recently, I recall there was the R-3.2.2 - and then I reverted back to > the "local" development environment. > > Federico > > On 03.03.16 10:08, Morgan, Martin wrote: >> Your description is not clear enough. See the github repository branch >> >> https://github.com/mtmorgan/PkgA/tree/import-conflict >> >> which imports NMF and ggplot2 without any warning during >> >> R CMD build PkgA >> R CMD check PkgA_0.0.1.tar.gz >> >> with >> >> $ R --version|head -n3 >> R Under development (unstable) (2016-02-27 r70232) -- "Unsuffered >> Consequences" >> Copyright (C) 2016 The R Foundation for Statistical Computing >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> >> ________________________________________ >> From: Federico Marini <mari...@uni-mainz.de> >> Sent: Thursday, March 3, 2016 3:44 AM >> To: Morgan, Martin; bioc-devel@r-project.org >> Subject: Re: [Bioc-devel] Imports, depends and warnings >> >> With the minimal working example, alone the importing of NMF raises the >> warning, so I guess this is due to that particular package. >> >> Should I contact the author of that in hope he adapts its NAMESPACE to >> have some nicer behavior? (or would be *just that* warning "fine" for >> the Bioc ecosystem?) >> >> >> Cheers, >> Federico >> >> >> On 02.03.16 20:41, Morgan, Martin wrote: >>> I think the only unavoidable case is when the package you import 'does it >>> wrong'. If that's not the case, then please provide an (easy-to-reproduce -- >>> start with a simple package.skeleton() and add a couple of Imports: and >>> import() statements, rather than providing your current package). >>> >>> Martin >>> >>> ________________________________________ >>> From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Federico >>> Marini >>> <mari...@uni-mainz.de> >>> Sent: Wednesday, March 2, 2016 10:53 AM >>> To: bioc-devel@r-project.org >>> Subject: [Bioc-devel] Imports, depends and warnings >>> >>> Hi Bioconductors, >>> >>> I'm on a good way to finalize the pcaExplorer package I presented at the >>> recent Bioc Developers Meeting. >>> >>> Trying to keep check and BiocCheck always in the background of my head, >>> as well as trying to be a good 'package neighbour', I am dealing with >>> the issue of some "Warning: replacing previous import by..." messages, >>> when building/loading/checking. >>> >>> From my understanding, there might be some cases where this can not be >>> fixed, probably because an imported package in turn imports itself >>> another one entirely, making my own import redundant (e.g., ggplot2 for >>> plotting and NMF for aheatmap give this part: >>> >>> Warnung: replacing previous import by ‘ggplot2::unit’ when loading ‘NMF’ >>> Warnung: replacing previous import by ‘ggplot2::arrow’ when loading ‘NMF’ >>> >>> This happens even if I specifically just use importFrom in the NAMESPACE. >>> >>> I'm kind of puzzled on this, so I thought I'd better ask out for some >>> expert advice on the ML. If required, I could put the package in a >>> GitHub repository. >>> >>> Thank you in advance for any help you can provide! >>> >>> Federico >>> >>> -- >>> Federico Marini, M.Sc. >>> Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) >>> Division Biostatistics and Bioinformatics >>> University Medical Center of the Johannes Gutenberg University Mainz >>> Postal address: 55101 Mainz >>> Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz >>> >>> Phone: +49 (0) 6131 17-8108 >>> Fax: +49 (0) 6131 17-2968 >>> Web: www.imbei.uni-mainz.de >>> E-Mail: mari...@uni-mainz.de >>> >>> _______________________________________________ >>> 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. >> -- >> Federico Marini, M.Sc. >> Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) >> Division Biostatistics and Bioinformatics >> University Medical Center of the Johannes Gutenberg University Mainz >> Postal address: 55101 Mainz >> Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz >> >> Phone: +49 (0) 6131 17-8108 >> Fax: +49 (0) 6131 17-2968 >> Web: www.imbei.uni-mainz.de >> E-Mail: mari...@uni-mainz.de >> >> >> 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. > > -- > Federico Marini, M.Sc. > Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) > Division Biostatistics and Bioinformatics > University Medical Center of the Johannes Gutenberg University Mainz > Postal address: 55101 Mainz > Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz > > Phone: +49 (0) 6131 17-8108 > Fax: +49 (0) 6131 17-2968 > Web: www.imbei.uni-mainz.de > E-Mail: mari...@uni-mainz.de > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
