[R] Setting bioconductor repository in .Rprofile. Is there a permanent way?

Kevin Wright kw.stat at gmail.com
Mon Jan 24 19:45:01 CET 2011


I currently set the Bioconductor repository in my .Rprofile using this
code (which needs editing for every version number change of
Bioconductor):

# Choose repositories
repos <- structure(c(CRAN="http://streaming.stat.iastate.edu/CRAN",
                     CRANextra="http://www.stats.ox.ac.uk/pub/RWin",
                     BioCsoft="http://www.bioconductor.org/packages/2.7/bioc",
                     Rforge="http://r-forge.r-project.org"))
options(repos=repos)
rm(repos)

I'd like to avoid editing the version number.  One hack to do so is
this code that adds all repositories.

setRepositories(ind=1:10)
r <- getOption("repos")
r <- r[!is.na(r)]
options(repos=r)

Is there a simpler way?  I've searched for quite a while without
finding an answer.


Incidentally, the help page for "options" says:
A Bioconductor mirror can be selected by setting
options("BioC_mirror"): the default value is
"http://www.bioconductor.org".
The word "default" is a bit confusing here, because when I start R, I see:

R> options()$BioC_mirror
NULL


-- 
Kevin Wright



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