[R] select repositories under linux

[Gabor Csardi]

Agreed, i had no idea that this is a Bioconductor package. 

G.

On Tue, Jan 22, 2008 at 09:49:50AM -0500, James W. MacDonald wrote:
> This is questionable advice for many CRAN packages, and horrible advice 
> for a Bioconductor package. If there are any dependencies (and BioC 
> packages often have many, and their dependencies may have 
> dependencies...) you can end up in download hell, all because you have 
> ignored the functionality that exists in R to handle such things.
> 
> As other posters have noted, you can use setRepositories(). You can also 
> set this in your .Rprofile file with something like
> 
> options(repos=(CRAN="http://ACloseRepository"))
> 
> so you don't have to do anything interactively.
> 
> Then use install.packages(), with dependencies=TRUE if you think there 
> may be dependencies (although I don't think it hurts if there are none).
> 
> For Bioconductor packages, use biocLite()
> 
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("GEOquery")
> 
> Best,
> 
> Jim
> 
> 
> Gabor Csardi wrote:
> >Eleni, download the package (I assume you know where it is), 
> >on Linux you will need the source package. Then from R type
> >
> >install.packages("<the file you downloaded>", repos=NULL)
> >
> >Gabor
> >
> >On Tue, Jan 22, 2008 at 11:26:12AM +0200, Eleni Christodoulou wrote:
> >>Hi all,
> >>
> >>I am trying to install the package "GEOquery" in unix. I have downloaded 
> >>the
> >>standard version of R and this package is not contained in the default. I
> >>know that I can select repositories under windows but I don't know how to 
> >>do
> >>it in unix. Does anyone have any idea on this?
> >>
> >>Thank you in advance,
> >>Eleni
> >>
> >>	[[alternative HTML version deleted]]
> >>
> >>______________________________________________
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> >>http://www.R-project.org/posting-guide.html
> >>and provide commented, minimal, self-contained, reproducible code.
> >
> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623

-- 
Csardi Gabor <csardi at rmki.kfki.hu>    UNIL DGM