Message-ID: <AANLkTi=eobf-3ZOA=zM69CqRxTHx6JgvjyqFssSwK8UF@mail.gmail.com>
Date: 2011-01-24T21:05:33Z
From: Kevin Wright
Subject: Setting bioconductor repository in .Rprofile. Is there a permanent way?
In-Reply-To: <AANLkTi=hOu=xOP0VuK+5x75G9hArsQ9Ab5fC+DJpL5uV@mail.gmail.com>
Now that is _simple_. Thanks.
Kevin
On Mon, Jan 24, 2011 at 1:49 PM, Kevin Wright <kw.stat at gmail.com> wrote:
> 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
>
--
Kevin Wright