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

[Henrik Bengtsson]

It is easier than that.  Use

http://www.bioconductor.org/packages/release/bioc

or

http://www.bioconductor.org/packages/devel/bioc

/Henrik

On Mon, Jan 24, 2011 at 10:56 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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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