----- Original Message ----- > From: "Florian Hahne" <florian.ha...@novartis.com> > To: "Hervé Pagès" <hpa...@fredhutch.org>, "Dan Tenenbaum" > <dtene...@fredhutch.org>, "Leonardo Collado Torres" > <lcoll...@jhu.edu> > Cc: bioc-devel@r-project.org > Sent: Wednesday, November 5, 2014 12:48:23 AM > Subject: Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC > 3.1 > > I think there is indeed something more fundamentally broken here: > > R.version > _ > platform x86_64-apple-darwin13.4.0 > arch x86_64 > os darwin13.4.0 > system x86_64, darwin13.4.0 > status Under development (unstable) > major 3 > minor 2.0 > year 2014 > month 10 > day 29 > svn rev 66895 > language R > version.string R Under development (unstable) (2014-10-29 r66895) > nickname Unsuffered Consequences > > > > useDevel(TRUE) > Error: 'devel' version already in use > >
The only problem is that you should not have seen this message, you should instead see a message saying you need a newer version of R to run the devel version of bioconductor. This has been fixed in the release version of BiocInstaller (1.16.1), available later today. > But: > > > biocinstallRepos() > BioCsoft > "http://bioconductor.org/packages/3.0/bioc" > BioCann > "http://bioconductor.org/packages/3.0/data/annotation" > BioCexp > "http://bioconductor.org/packages/3.0/data/experiment" > BioCextra > "http://bioconductor.org/packages/3.0/extra" > CRAN > "http://cran.fhcrc.org" > > > So I am running R-devel, R thinks that I should already be using the > BiocDevel branch, but the repository is still pointing to > Bioconductor 3.0 > After taking a closer look at useDevel() I did this: > > assignInNamespace(ns="BiocInstaller", x="IS_USER", value=TRUE) > assignInNamespace(ns="BiocInstaller", x="IS_UPGRADEABLE", value=TRUE) > > > > And behold: > > useDevel(TRUE) > Installing package into > Œ/Users/hahnefl1/software/R/source/R-3-2-0/localPackages¹ > (as Œlib¹ is unspecified) > trying URL > 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocInstaller_1.17.1 > .tar.gz' > Content type 'application/x-gzip' length 14271 bytes (13 KB) > opened URL > ================================================== > downloaded 13 KB > > * installing *source* package ŒBiocInstaller¹ ... > ** R > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help > * DONE (BiocInstaller) > > The downloaded source packages are in > Œ/private/tmp/Rtmp44wF3Y/downloaded_packages¹ > Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help > 'BiocInstaller' changed to version 1.17.1 > > > I couldn't tell how I got my R installation into this seemingly > locked > state, but maybe there should be a force=TRUE option to useDevel for > cases > like this. > Florian > > This is NOT what you want. You now have Bioc 3.1 on R 3.1, but Bioc 3.1 is intended to run with R-devel (3.2) only. Dan > > > > On 04/11/14 20:04, "Hervé Pagès" <hpa...@fredhutch.org> wrote: > > >Hi, > > > >On 11/02/2014 10:58 PM, Dan Tenenbaum wrote: > >> > >> > >> ----- Original Message ----- > >>> From: "Leonardo Collado Torres" <lcoll...@jhu.edu> > >>> To: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com> > >>> Cc: bioc-devel@r-project.org > >>> Sent: Sunday, November 2, 2014 9:26:25 PM > >>> Subject: Re: [Bioc-devel] Can't seem to use useDevel(); > >>> biocLite() for > >>>BioC 3.1 > >>> > >>> Thanks, I incorrectly thought that I was using the same R version > >>> as > >>> the Bioc-build machines since the "r66923" part matched. Now I > >>> realize > >>> that this tag is used in all of the newest R builds at > >>> http://r.research.att.com/. > >>> > >> > >> It's admittedly confusing; > > > >Agreed. But the error message issued by useDevel() in the current > >release adds to the confusion: > > > > > library(BiocInstaller) > > Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for > > help > > > useDevel() > > Error: 'devel' version already in use > > > >What about something like: > > > > Error: you need R 3.2 to run BioC 'devel' version > > > >Thanks, > >H. > > > >> the question of whether to use R-devel with Bioc-devel has a > >> different > >>answer every six months, but the answer can always be found here: > >> > >> http://www.bioconductor.org/developers/how-to/useDevel/ > >> > >> Also, when looking at the devel build report, you should probably > >> focus > >>more on the version portion of the "R version" column than on the > >>SVN > >>revision number. > >> > >> Dan > >> > >> > >>> On Sun, Nov 2, 2014 at 9:57 PM, Kasper Daniel Hansen > >>> <kasperdanielhan...@gmail.com> wrote: > >>>> You should not be using R-3.1.2 patched with the current devel > >>>> version of > >>>> Bioconductor; use R-devel. > >>>> > >>>> Best, > >>>> Kasper > >>>> > >>>> On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres > >>>> <lcoll...@jhu.edu> > >>>> wrote: > >>>>> > >>>>> Hi, > >>>>> > >>>>> I can't seem to install devel packages via biocLite() and I > >>>>> wonder > >>>>> if > >>>>> something is broken or if I'm missing something. For example, > >>>>> take > >>>>> GenomeInfoDb which is at 1.3.6 and is passing all checks. > >>>>> > >>>>> The usual code using a fresh R 3.1.2-patched install isn't > >>>>> working > >>>>> as > >>>>> it downloads the latest release version (1.2.2): > >>>>> > >>>>>> source("http://bioconductor.org/biocLite.R") > >>>>> Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for > >>>>> help > >>>>> ## Was expecting 3.1 here > >>>>>> useDevel() > >>>>> Error: 'devel' version already in use > >>>>>> biocLite('GenomeInfoDb') > >>>>> BioC_mirror: http://bioconductor.org > >>>>> Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R > >>>>> version > >>>>> 3.1.2. > >>>>> Installing package(s) 'GenomeInfoDb' > >>>>> trying URL > >>>>> > >>>>>'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/Geno > >>>>>meInfoDb_1.2.2.tgz' > >>>>> Content type 'application/x-gzip' length 404120 bytes (394 KB) > >>>>> opened URL > >>>>> ================================================== > >>>>> downloaded 394 KB > >>>>> > >>>>> > >>>>> The downloaded binary packages are in > >>>>> > >>>>> > >>>>>/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//Rtmpxp29xo/downloade > >>>>>d_packages > >>>>>> > >>>>>> sessionInfo() > >>>>> R version 3.1.2 Patched (2014-11-01 r66923) > >>>>> ## Note that it matches the current R version used by the > >>>>> Bioc-devel > >>>>> build machines > >>>>> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >>>>> > >>>>> locale: > >>>>> [1] > >>>>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >>>>> > >>>>> attached base packages: > >>>>> [1] stats graphics grDevices utils datasets methods > >>>>> base > >>>>> > >>>>> other attached packages: > >>>>> [1] BiocInstaller_1.16.0 colorout_1.0-2 > >>>>> > >>>>> loaded via a namespace (and not attached): > >>>>> [1] tools_3.1.2 > >>>>> > >>>>> > >>>>> > >>>>> For my computer it's not problem because I can download the pkg > >>>>> via > >>>>> svn and install locally. But it breaks my tests in TravisCI > >>>>> which > >>>>> relies on biocLite(). > >>>>> > >>>>> Cheers, > >>>>> Leo > >>>>> > >>>>> _______________________________________________ > >>>>> 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 > >>> > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > >-- > >Hervé Pagès > > > >Program in Computational Biology > >Division of Public Health Sciences > >Fred Hutchinson Cancer Research Center > >1100 Fairview Ave. N, M1-B514 > >P.O. Box 19024 > >Seattle, WA 98109-1024 > > > >E-mail: hpa...@fredhutch.org > >Phone: (206) 667-5791 > >Fax: (206) 667-1319 > > > >_______________________________________________ > >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