R help - Jan 2011 - Setting bioconductor repository in .Rprofile. Is there a permanent way?

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

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
> 
> 

-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

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