Wednesday, July 20, 2016

Problems installing latest R version on cluster

For my research, I often need to access R on a cluster instead of on my personal laptop. This week I tried to update to the latest version of R-3.3.1 and I found out it is no longer as simple as it used to be. Previously, I would just follow my notes on installing R and R packages locally which is posted on GitHub. To install the latest R (currently version 3.3), I needed to access newer versions of some libraries (zlib, bzip2, curl, pcre and xz). The './configure' step would fail without access to the updated libraries. Usually these types of packages would be included in the installation of R on linux, but it is no longer included. Instead, it assumes these libraries are already installed and updated.

This led to some frustration. Then a postdoc in our lab (Mike Love) sent me this wonderful step-by-step tutorial on getting the updated libraries and successfully installing the latest R. As the tutorial mentions, if the system admins update these libraries, you won't run into this problem. If they don't keep this libraries up-to-date, then you will find this tutorial to be very helpful.

P.S. I tweeted the link and Gabe Becker responded that he had a more complicated set up. His solution was to statically link to the libraries.

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