How to add packages to your local repository

Depending on the packages you want installed, you can do one of two things within R. First we load the R module and run R:

[abc123@login01 ]$ module load R/3.5.1
[abc123@login01 ]$ R

For BioConductor packages, type the following:


Install specific packages, e.g., “GenomicFeatures” and “AnnotationDbi”, with

biocLite(c("GenomicFeatures", "AnnotationDbi"))

The biocLite() function (in the BiocInstaller package installed by the biocLite.R script) has arguments that change its default behavior; type ?biocLite for further help. For more information regarding the BioConductor package, please visit their Installation website here https://www.bioconductor.org/install/

For CRAN packages, type the following:


How to use R or Rstudio on Shamu

Now that you have your packages installed, you have two (2) ways of using R on Shamu, interactively or non-interactive.


Below is a sample submit script that you can edit for your R input file and submit with qsub name_of_this_file.qsub. This sample assumes you are using R in parallel mode and requesting 20 cores.

#$ -S /bin/bash
#$ -N Name_of_job
#S -q all.q
#$ -cwd
#$ -j y
#$ -o $JOB_ID.log
#$ -pe threaded 20
. /etc/profile.d/modules.sh
# Load one of these
module load shared R/3.4.0
R -e "source('Script_Simulation_2_15_65.R')"


Grab a compute node with qlogin, load the rstudio module and run the rstudio program:

[abc123@login01 ~]$ qlogin
[abc123@compute015 ~]$ module load R/3.5.1 rstudio
[abc123@compute015 ~]$ rstudio

Using R in parallel mode

Your R input file must contain the parallel() section for parallel execution of R binaries to work properly. Here is an example:
require(parallel); require(mvtnorm); set.seed(2000)
cat('Cores: ', detectCores(), '\n')

-- AdminUser - 26 Jul 2017
Topic revision: r7 - 23 Oct 2018, AdminUser
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