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May/081
May/081
Installing R/BioConductor on Ubuntu 8.04
The new version of Ubuntu is out, (as if you haven’t heard that by now), so that means a fresh install to play about with and working just the way I want! 
One of the tools that I currently need (for the thesis work) is R and the BioConductor libraries. So here’s a quick run down on getting them up and installed on Hardy…
First up, run these commands in a terminal:
sudo apt-get install build-essential g77 gfortran
sudo apt-get install refblas3 refblas3-dev zlib1g-dev
sudo apt-get install r-base
This will then install the R base packages and some of the BioConductor packages, along with the gcc and fortran compilers and some other libraries that will be required for the next step.
sudo -s
R
Now at the R prompt, type the following…
source("http://www.bioconductor.org/biocLite.R")
biocLite()
Now sit back for a few minutes while your system configures BioConductor for you.
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6:31 pm on July 24th, 2008
I wanted to add a small enhancement to the instructions noted above. The instructions are correct as written, but the Ubuntu repositories do not have the latest production release of R, which may be required for your analysis work. For example, R-2.6.2 is available today from Ubuntu, but R-2.7.1 is available from CRAN. This change would prevent someone from using the latest Bioconductor version 2.3, which requires R-2.7.
Here is the reference: http://cran.r-project.org/bin/linux/ubuntu/README The key step is the addition of the R-mirror which overrides the Ubuntu repository, and provides access to the latest production release. I used: http://cran.wustl.edu/bin/linux/ubuntu/hardy/
Hope this information helps someone!