What are the major changes to the R environment?

There are a number of important changes now that the Linux operating system on the SCC has been upgraded to CentOS 7. Newer versions of R have been installed, with many popular R packages. The newest version of rstudio is now also available on the SCC.

R Versions

As of June 12, 2019 there are four R versions installed on the SCC: R/3.0.0, R/3.5.1, R/3.6.0, and R/3.6.0_intel-2018. As always you can check available versions of R by executing the module avail R command.

None of these versions require the gcc module to be loaded. Please check your submission scripts, adjust the version of R, and remove any module load gcc commands.

The default R module is R/3.6.0. The former default module R/3.2.3 and many other older versions of R are no longer available. Please contact us if your workflow requires an R version that is no longer available on the SCC.

As always, R packages can be installed in your home directory.

If you previously used the R/3.5.0 or R/3.5.2 version and plan to use the R/3.5.1 version, you might need to re-install some packages that you previously installed as they may no longer load correctly in the new environment.

RStudio Module

RStudio is no longer available without loading a module. A newer version of this application is available – rstudio/1.2.1335. To use it, load both the R and rstudio modules:

scc1% module load R/3.6.0
scc1% module load rstudio
scc1% rstudio &

R Packages Prerequisites

R packages no longer need any module prerequisites. For example previously, to use the rjags package you had to run module load jags/3.4.0. Now you only need to load the R version of your choice:

scc1% module load R/3.6.0

Troubleshooting

  • Review module load commands in your batch scripts and change the version of the R module to one that is currently available.
  • There are no longer any prerequisites for R. For example, the gcc module no longer needs to be loaded.
  • Check if the R packages you use in your R code are installed. If needed, install them in your home directory or email help@scc.bu.edu for assistance.