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