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

[Kevin Wright]

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