Taking a closer look at your email... > ----- Original Message ----- > > From: "Florian Hahne" <florian.ha...@novartis.com> > > > 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 > >
Sorry, didn't notice you were already running R-devel. > > > > > useDevel(TRUE) > > Error: 'devel' version already in use > > > > What version of BiocInstaller were you running at this point> > > 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 > > > > > I think you somehow had the release version of BiocInstaller installed in R-devel. But it's difficult to know now.... Dan > > 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 > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
