[Bio-Linux] How to get full functionality from R and BioConductor on a multi-user Bio-Linux system

[Bela Tiwari]

Hello

As some of you, or your users may have noticed, fucntions in the R and
BioConductor packages sometimes need to download other packages and
files and by default will try to put these in /usr/lib/R/library, which
is only writable by root.

There is an easy way to make these functions download to directories
writable by the user and we have written information about this on the
following web page:

http://envgen.nox.ac.uk/envgen/software/archives/000455.html 


The basic information on this topic is copied below, but there is more
detail on the web page, including further details about how and why this
works.

Please note that the line referred to as being in 
/usr/software/bioenvrc  in the instructions below  is only present in
the copies of that file obtained from us from now on - it won't be in
any of your files at this point!


cheers


Bela


The recommended way to set up Bio-Linux to allow users to get the full
functionality of R and BioConductor involves two steps:

1) Create a directory the user can write to. For example, the user
could type:

mkdir ~/myRlib

2) Set the R_LIBS environmental variable to this directory:

This can be done by a user manually each time they want to use R, by
typing:

setenv R_LIBS ~/myRlib

or it can be set automatically each time the user logs in; there are a
variety of ways to do this. On Bio-Linux, you could set this variable in
your /usr/software/bioenvrc file. The most recent images of Bio-Linux
include this variable in that file - if you remove the hash in front of
the line, the variable will be set when any user logs in.

Please note - make sure that if you unhash the line in
/usr/software/bioenvrc that the directory name listed there is the same
as the name you have chosen for the directory R will be writing to. 





*************************
Dr. Bela Tiwari
Lead Bioinformatician

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

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