bioconductor/devel_sequencing is updated now. 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: Monday, March 7, 2016 12:21:41 AM > Subject: Re: [Bioc-devel] Imports, depends and warnings > Thanks for looking into it! > Still saves some time in installing R-devel (and always provides a fresh > one). > > Federico > > On 04.03.16 23:48, Dan Tenenbaum wrote: >> 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 > > -- > 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