[BioC] Installing Bioconductor with 'sudo' privilege

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Sep 1 16:57:28 CEST 2009

Hi Sharon,

On Sep 1, 2009, at 10:29 AM, Sharon wrote:

> Hi,
> I am allowed to install programs thro' sudo on my LINUX server. I have
> installed R 2.9.0 and trying to install bioconductor.  As expected,  
> when I
> tried to install bioconductor inside R, it says 'lib =
> "/usr/lib64/R/library"' is not writable. This means, I have to  
> download the
> source of each package and install using R CMD INSTALL. Is there any  
> other
> elegant way of installing bioconductor with 'sudo' privilege?

Can you just sudo-launch R? That should give you the appropriate privs  
to then install packages "in the normal way," no?


$ sudo R
## do password song and dance
## ... welcome to R ...
R> source('http://bioconductor.org/biocLite.R')
R> biocLite(c('some', 'packages'))


Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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