That might well be. I can't recall doing anything special, but I'll try to uninstall BiocInstaller the next time I run into a similar issue to test this. Florian
On 05/11/14 18:02, "Dan Tenenbaum" <dtene...@fredhutch.org> wrote: >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/Ge >>>>>>>no >> > >>>>>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/downloa >>>>>>>de >> > >>>>>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