Yes, it looks like devel_sequencing has not updated for a while. I'll look into that. Dan
----- Original Message ----- > From: "Federico Marini" <mari...@uni-mainz.de> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Martin Morgan" <martin.mor...@roswellpark.org>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Friday, March 4, 2016 1:40:54 PM > Subject: Re: [Bioc-devel] Imports, depends and warnings > Hi Dan, > > I pulled the devel_sequencing image - took the most up to date a couple of > days > ago. > Probably even if the rocker/rstudio-daily is indeed updated daily the bioc > container isn't? > > Federico > ________________________________________ > From: Dan Tenenbaum <dtene...@fredhutch.org> > Sent: Friday, March 4, 2016 10:05 PM > To: Marini, Federico > Cc: Martin Morgan; bioc-devel > Subject: Re: [Bioc-devel] Imports, depends and warnings > > 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
