[R] select repositories under linux

[James W. MacDonald]

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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> 

-- 
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