Entering edit mode
Dan Swan
▴
10
@dan-swan-792
Last seen 10.1 years ago
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,
/usr/lib/R/library/liblisting
.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
http://www.bioconductor.org/data/cd
fenvs/repos/"
[1] "Download complete."
[1] "Installing mgu74av2cdf"
mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission
denied
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,
/usr/lib/R/library/liblisting
.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,
Dan
--
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@ceh.ac.uk