[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
----- Original Message -----
From: "Leonardo Collado Torres" <lcollado at jhu.edu> To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com> Cc: bioc-devel at 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 <kasperdanielhansen at 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 <lcollado at 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
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