[BioC] writing of /usr/lib/R

James W. MacDonald jmacdon at med.umich.edu
Tue Nov 8 14:58:27 CET 2005

Hi Michael,

Note that this question is more applicable to R-help 
<r-help at stat.math.ethz.ch> rather than BioC, since it concerns 
R-administration rather than a particular BioC package.

Anyway, there are (at least) two ways around this problem that don't 
involve making /usr/local writable by normal users.

First, if there are not that many users, they can always install R in 
their /home/username directory (e.g., ./configure and make, but no make 
install). This is preferable in many ways due to the fact that R and 
BioC are released semi-annually, which can make your job a pain if the 
end users are constantly wanting the latest version. Of course this will 
require that each user have enough disk space allotted to them. I think 
this is probably the most common way to do things.

Second, you could simply install R in the same fashion to a directory 
where everybody has write privileges. This has the advantage of using 
less disk space, but you then run the risk of people changing the 
installation in ways that adversely affect other users.



Michael Green wrote:
> New to the list, first post!
> I'm doing sysadmin work for our Bioinformatics department where I
> manage a couple of IBM BladeCenter based clusters. Systems are running
> SLES9 SP1 i586 (dual Xeon 32bit).
> Before I'm going to ask my question I must admit that I'm complete
> novice to R, and since I won't use it myself I didn't read much of the
> documentation supplied with the package. My question is more related
> to system administration + R, rather then to R itself.
> So here it is:
> Some time ago I received a request from our users to install R on one
> of the clusters.
> I went ahead and installed R-base-2.1.0-1 supplied by the vendor (SuSE/Novell).
> After that following the request of the users, I installed the
> Bioconductor packages using the standard procedure described at
> <http://www.bioconductor.org/download>:
> source("http://www.bioconductor.org/biocLite.R")
> biocLite()
> Soon thereafter it became apparent that during their work with R, our
> users need to install/uninstall or otherwise change the hierarchy
> under /usr/lib/R  which is of course not writable by any user other
> than root. As you surely know that's the case for almost every
> directory under /usr. From talking to one of my users I've learned
> that R routinely downloads/installs/updates itself and the changes go
> into /usr/lib/R exclusively (or almost exclusively?).
> Now I'm faced with dilemma of how to allow users to write to
> /usr/lib/R, which is not a big deal on itself as there are at least a
> couple of ways doing that:
> 1. Play with standard unix permissions: create a new group for R
> users; chgrp <that_group> /usr/lib/R. etc...
> 2. Create ACL for /usr/lib/R
> But my question is not about how to make /usrlib/R writable, but this:
> since /usr and everything under it is not traditionally writable by
> regular users what's the official stance of R developers on this? Is
> it assumed that all R users should have root access to the system
> where R installed to be able to change contents of /usr/lib/R and
> actually do any useful work?
> About our R installation:
> bioinfo4:/usr/lib/R # R
> R : Copyright 2005, The R Foundation for Statistical Computing
> Version 2.1.0  (2005-04-18), ISBN 3-900051-07-0
> R version 2.1.0, 2005-04-18, i686-pc-linux-gnu
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "base"
> --
> Warm regards,
> Michael Green
> _______________________________________________
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> Bioconductor at stat.math.ethz.ch
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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