Setting bioconductor repository in .Rprofile. Is there a permanent way?
Of course, before posting my question, I did RTFM and RTFcode and
RTFmailinglists. The key word in my question was "simpler". I
rejected copying a modified version of the "repositories" file to my
home directory since it has changed numerous times with addition of
"R-forge" etc.
Here is another option. More lines of code, but doesn't add unneeded
repositories.
pp <- file.path(R.home("etc"), "repositories")
rr <- tools:::.read_repositories(pp)
repos <- structure(c(CRAN="http://streaming.stat.iastate.edu/CRAN",
CRANextra="http://www.stats.ox.ac.uk/pub/RWin",
BioCsoft=rr["BioCsoft","URL"],
Rforge="http://r-forge.r-project.org"))
options(repos=repos)
rm(pp, rr, repos)
Martin, I appreciated your clever trick of evaluating on demand.
Kevin
On Mon, Jan 24, 2011 at 12:45 PM, Kevin Wright <kw.stat at gmail.com> 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: R> options()$BioC_mirror NULL -- Kevin Wright
Kevin Wright