Installing R packages on the HPC (Not Needed Today)
When you come to running your own R scripts on the HPC, you will need to install the packages your script needs. We have done this for you for this training session but to install your own packages you can follow a procedure like this:
First, in RStudio create a new R script (File → New File → R script), and save as install.R
# This line will use the Canberra mirror for CRAN
chooseCRANmirror(graphics = getOption("menu.graphics"), ind = 3, local.only = TRUE)
# Sometimes you need to install packages from github, like this:
install.packages("devtools")
devtools::install_github("YuLab-SMU/ggtree")
# Sometimes you have
bioconductor_packages <- c("clusterProfiler", "pathview", "AnnotationHub", "org.Hs.eg.db")
cran_packages <- c("tidyverse", "ggplot2", "plyr", "readxl", "scales")
# Compares installed packages to above packages and returns a vector of missing packages
new_packages <- bioconductor_packages[!(bioconductor_packages %in% installed.packages()[,"Package"])]
new_cran_packages <- cran_packages[!(cran_packages %in% installed.packages()[,"Package"])]
# Install missing bioconductor packages
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager", version = "3.16")
BiocManager::install(new_packages, dependencies = TRUE, INSTALL_opts = '--no-lock')
# Install missing cran packages
if (length(new_cran_packages)) install.packages(new_cran_packages, repos = "https://cran.csiro.au/")
# Update all installed packages to the latest version
update.packages(bioconductor_packages, ask = FALSE)
update.packages(cran_packages, ask = FALSE, repos = "https://cran.csiro.au/")
Then, in RStudio create a new Text File (File → New File → Text File), and save as install.pbs
#!/bin/bash -l
#PBS -N R_install
#PBS -l select=1:ncpus=1:mem=4gb
#PBS -l walltime=2:00:00
#PBS -m abe
cd $PBS_O_WORKDIR
module purge
module load r/4.2.2-foss-2022b
mkdir -p $PBS_O_WORKDIR/r_library
export R_LIBS_USER="${PBS_O_WORKDIR}/r_library"
echo $R_LIBS_USER
Rscript install.R
Run this on the HPC:
# Convert the launch_R.pbs to Linux format dos2unix install.pbs # Submit the job to the HPC qsub install.pbs # Check the status of the job qjobs