----- 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; 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/GenomeInfoDb_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/downloaded_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