[BioC] Bioconductor setup

Dan Swan dswan at ceh.ac.uk
Thu Jun 3 17:51:57 CEST 2004

Hi there,

We supply Bioconductor as part of the Bio-Linux project 
(http://bio-linux.net).  This is a modified Linux distro for 
bioinformatics.  Often when deployed the machines act as multi-user servers.

R has been installed on the system (1.9.0) as a root equivalent user. 
Bioconductor was installed via getBioC with R running as a root 
equivalent user.

The problem we have is that people who then run Bioconductor from their 
own unprivledged accounts start to run into permissions issues when 
routines such as read.affybatch decide they want to start writing to the 
library directories:

 > read.affybatch(filenames = listofiles)
Loading required package: reposTools
Warning messages:
1: Incompatible phenoData object. Created a new one.
  in: read.affybatch(filenames = listofiles)
2: Incorrect permissions to edit package database, 
.Rda in: save.locLib(locLibList, curLib)
Note: You did not specify a download type.  Using a default value of: Source
This will be fine for almost all users

[1] "Attempting to download mgu74av2cdf from 
[1] "Download complete."
[1] "Installing mgu74av2cdf"
mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission 
ERROR: failed to lock directory '/usr/lib/R/library' for modifying
Error in library("mgu74av2cdf", lib.loc = "/usr/lib/R/library") :
         There is no package called 'mgu74av2cdf'
In addition: Warning messages:
1: Incorrect permissions to edit package database, 
.Rda in: save.locLib(locLibList, curLib)
2: Installation of package mgu74av2cdf had non-zero exit status in: 
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)

Now the /usr/lib/R/library subdirectories are owned, grouped and only 
writable by root hence the errors being spat out.

I can't obviously have R installs for every user, but I'm starting to 
wonder if each user on the system requires their own Bioconductor 
install in their own workspace?

I have thought about chgrping the directory to a new gid and adding 
Bioconductor users to that group, which may work, but is an ugly kludge.

I'm not familiar with R or Bioconductor - so if there is a simple 
solution (like specifying a temporary working directory when these 
operations are performed, or setting some kind of environmental variable 
that R understands) I would be delighted to know :)

many thanks in advance,


Dr Dan Swan - Bio-Linux Developer | RHCE
EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR
Tel: 01865 281 658 Fax: 01865 281 696
http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk

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