[R] 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()$BioC_mirror NULL -- Kevin Wright __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Setting bioconductor repository in .Rprofile. Is there a permanent way?
On 01/24/2011 10:45 AM, Kevin Wright wrote:
I currently set the Bioconductor repository in my .Rprofile using this
code (which needs editing for every version number change of
Bioconductor):
# Choose repositories
repos - structure(c(CRAN=http://streaming.stat.iastate.edu/CRAN;,
CRANextra=http://www.stats.ox.ac.uk/pub/RWin;,
BioCsoft=http://www.bioconductor.org/packages/2.7/bioc;,
Rforge=http://r-forge.r-project.org;))
options(repos=repos)
rm(repos)
I'd like to avoid editing the version number. One hack to do so is
this code that adds all repositories.
setRepositories(ind=1:10)
r - getOption(repos)
r - r[!is.na(r)]
options(repos=r)
Is there a simpler way? I've searched for quite a while without
finding an answer.
Incidentally, the help page for options says:
A Bioconductor mirror can be selected by setting
options(BioC_mirror): the default value is
http://www.bioconductor.org;.
The word default is a bit confusing here, because when I start R, I see:
one possibility is to
source('http://bioconductor.org/biocLite.R')
in .Rprofile, after which biocinstallRepos() provides the correct bioc
repositories for the version of R in use; it does clutter the .GlobalEnv
a little and would be irritating if, e.g., on a laptop, internet access
were slow or not reliable. For the latter I wrote
makeActiveBinding(biocLite, local({
env - new.env()
function() {
if (!exists(biocLite, envir=env, inherits=FALSE)) {
evalq(source(http://bioconductor.org/biocLite.R;,
local=TRUE),
env)
}
env[[biocLite]]
}
}), .GlobalEnv)
which doesn't make the connection until one accesses the biocLite variable.
Martin
R options()$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
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] 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.s...@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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Setting bioconductor repository in .Rprofile. Is there a permanent way?
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 mtmor...@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
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Setting bioconductor repository in .Rprofile. Is there a permanent way?
Now that is _simple_. Thanks. Kevin On Mon, Jan 24, 2011 at 1:49 PM, Kevin Wright kw.s...@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.s...@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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
