Setting bioconductor repository in .Rprofile. Is there a permanent way?
On 01/24/2011 10:45 AM, Kevin Wright wrote:
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:
one possibility is to
source('http://bioconductor.org/biocLite.R')
in .Rprofile, after which biocinstallRepos() provides the correct bioc
repositories for the version of R in use; it does clutter the .GlobalEnv
a little and would be irritating if, e.g., on a laptop, internet access
were slow or not reliable. For the latter I wrote
makeActiveBinding("biocLite", local({
env <- new.env()
function() {
if (!exists("biocLite", envir=env, inherits=FALSE)) {
evalq(source("http://bioconductor.org/biocLite.R",
local=TRUE),
env)
}
env[["biocLite"]]
}
}), .GlobalEnv)
which doesn't make the connection until one accesses the biocLite variable.
Martin
R> options()$BioC_mirror NULL
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