[BioC] Repository for Bioconductor annotation packages
James W. MacDonald
jmacdon at med.umich.edu
Sat Jul 15 13:53:55 CEST 2006
Daniel Gatti wrote:
> Daniel Gatti wrote:
>
> >> O/S: Linux
> >> arch : i686
> >> R version : 2.2.1
> >>
> >> I'm using the install.packages() command to install Bioconductor
> >> libraries to my home directory. I can install functional packages like
> >> "safe" and "GOstats". But when I try to install annotation packages, it
> >> tells me that it can't find them in given repository. I'm using
> >> repos="http://www.bioconductor.org". What repository should I use for
> >> the annotation packages?
> >>
> >> install.packages("hgu133a", lib = "~/Rlib",
> >> repos="http://www.bioconductor.org")
>
> >It's easier to use biocLite() instead.
> >
> >source("http://www.bioconductor.org/biocLite.R")
> >biocLite("hgu133a")
>
> biocLite installs in the R library directory on the server.
That's not true. biocLite() is simply a wrapper to install.packages()
that among other things sets the correct repositories to iterate
through. All you have to do is pass a lib argument and it will install
wherever you want, just like install.packages().
> biocLite("affy", lib="C:/Documents and Settings/dd1/Desktop/test")
Running getBioC version 0.1.6 with R version 2.3.0
Running biocinstall version 1.8.4 with R version 2.3.0
Your version of R requires version 1.8 of Bioconductor.
trying URL
'http://bioconductor.org/packages/1.8/bioc/bin/windows/contrib/2.3/affy_1.10.0.zip'
Content type 'application/zip' length 2230953 bytes
opened URL
downloaded 2178Kb
package 'affy' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Documents and Settings\dd1\Local
Settings\Temp\RtmpM8Sbqb\downloaded_packages
updating HTML package descriptions
> dir("C:/Documents and Settings/dd1/Desktop/test")
[1] "affy"
--
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623
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