Hello,

We are in the midst of changing our SOP for R on our local cluster. Network access is only available from the head node but we don't want users downloading and compiling packages on the head node. Previously, we asked that all package installations & updates be done by the admins on request but this is unsustainable. We've decided to internally mirror both CRAN and Bioconductor and keep a core of the most used packages on R_HOME/library and update those weekly. Users can also download/install/update other packages from CRAN/Bioconductor using their own local library. What we are trying to work out now are the system settings needed so that install.packages (and eventually biocLite) automatically point to only our internal mirrors without having specify them in the repos argument. After much googling, I think I've figured out that we need to set up a ~R/etc/Rprofile.site file to change the default CRAN repository to our local site using options(repos = c(CRAN = "file:////home/mirrors/no_backup/cran"). Is this all that is needed or do we also need to modify ~R/etc/repositories, changing the URL locations to our local ones and commenting out the other repositories? Anything else we need to do to get install.packages("ape") to work seamlessly for the end user? We want to make it so that only users who really know what they are doing can get around installing from the local mirrors, even if they are accidentally running on the head node.

Thanks for any help or suggestions,
Jenny

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
High Performance Biological Computing Program
and The Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign
NOTE NEW OFFICE LOCATION
2112 IGB
1206 W. Gregory Dr.
Urbana, IL 61801
USA
ph: 217-300-6543
fax: 217-265-5066
e-mail: drnevich@illinois.edu<mailto:drnevich@illinois.edu>


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