[Bio-Linux] IMPORTANT - All users of R on Bio-Linux 5

[Tim Booth]

Dear All,

A new version of R (2.9.0) is due to be released tomorrow (April 17
2009).  Because Bio-Linux 5 is set to pick up software updates from the
CRAN package server in Bristol this update will be installed
automatically.  Unfortunately, several modules - notably those that are
part of Bioconductor - are not yet officially updated to support this
version.  Therefore Bioconductor will be unavailable if the update goes
ahead.  If you are using Bioconductor right now you have three options:

1) Hold off the update by editing your sources.list.  Give the command:

        nano -w /etc/apt/sources.list
        
        Place a hash (#) in front of the final line (the one referencing
        www.stats.bris.ac.uk/R/ ) and save the file.

2) If you do update R, you can install a pre-release of the new 
        Bioconductor modules by using the package created by Philip de
        Groot.  Download the file from here:
        
        http://nebc.nox.ac.uk/downloads/bio-linux/gp-bioc-2.4-0_i386.deb
        
        Then run 'sudo dpkg -i gp-bioc-2.4-0_i386.deb'

3) If you do not require the bioconductor modules in the next few days:

        Official support for Bioconductor in R 2.9 is due for release
        next week, on April 21st.  Therefore over the next few days we
        will be preparing and testing full instructions for making a
        smooth upgrade to the official release and sending them out on
        this list and on our website.
        
In the meantime, if you have any problems or concerns please contact us
via the helpdesk address - helpdesk at nebc.nox.ac.uk.

Thanks,

Tim

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Oxford
+44 1865 281 975