So a preliminary diagnosis is that some packages are not building even though they build in the nightly builds. The problem could be a newer compiler, newer R-devel, slightly different OS (debian vs ubuntu) or something else. Investigating further. However, in the meantime, bioconductor/devel_base is now up to date. Of course this only includes one Bioconductor package (BiocInstaller) and fewer system dependencies, but it might be a helpful stopgap for you.
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 1:48:45 PM > Subject: Re: [Bioc-devel] Imports, depends and warnings > Thanks! > > In the meanwhile I went for a DIY solution - but it would be great to have the > image again up(dated) and running. > > Federico > ________________________________________ > From: Dan Tenenbaum <dtene...@fredhutch.org> > Sent: Friday, March 4, 2016 10:46 PM > To: Marini, Federico > Cc: Martin Morgan; bioc-devel > Subject: Re: [Bioc-devel] Imports, depends and warnings > > 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