[Bio-Linux] Updating R and Bioconductor on Bio-Linux

[Bela Tiwari]

Hello,

This email is to follow up on our email last week about R and
Bioconductor on Bio-Linux.

R 2.9.0 and Bioconductor 2.4 are now available. If you wish to ensure 
that all your R and Bioconductor libraries are up to date, you can run
the commands below. If you chose option 1 in the previous email, and
stopped the updates from happening, you should remove the hash you put
in front of the line that includes www.stats.bris.ac.uk/R/, then update
R, or wait until the updates are run overnight. Then follow the
instructions below.  If you chose option 2, and installed Philip de Groot's package, there 
are a few notes about that package at the very end of this email. 

Commands to run:

sudo R

Then at the R command prompt, type:

source("http://bioconductor.org/biocLite.R")
update.packages(repos=biocinstallRepos(), ask=FALSE)

The update will take some time. You may see errors at the end when the
rgl package attempts to update. This package was originally installed
using the r-cran-rgl package. If you don't use rgl, or are happy with
version 0.76, which is currently installed, then you can ignore this.

If you want the latest version, which is 0.84, then instructions follow:

Installing rgl via R:
You can get the latest version of rgl by using the R command
install.packages("rgl")
However, BEFORE you do this, you will need to install some libraries.
You can do this by typing on a terminal command line (not R):

sudo apt-get install libglu1-mesa-dev

(This will install the libglu1-mesa-de, libgl1-mesa-dev and
mesa-common-dev packages.)

If you choose to update rgl this way, it should not conflict with the
version installed via the deb package r-cran-rgl on a standard Bio-Linux
system, and the version you installed from within R should take
precedence. Note that the r-cran-rgl package is required by Rcommander,
so is best left installed if you or other users of your system use
Rcommander.


Further notes about Philip de Groot's package:
Philip has just informed us that 2 of the R libraries in his package have slight alterations compared to the version from CRAN. These are:

 - simpleaffy - changed so that tab characters are interpreted as proper separators when loading a covdesc file. 
 - q-value - removal of the tcltk dependency so that servers without X11 output do not crash when loading this library



*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************