Content Comparison

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)
# 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/")

#!/bin/bash -l
#PBS -N R_install
#PBS -l select=1:ncpus=1:mem=4gb
#PBS -l walltime=2:00:00
#PBS -m abe

module purge
module load r/4.2.12-foss-2022a2022b
cd $PBS_O_WORKDIR
mkdir -p r_library
export R_LIBS_USER='$PBS_O_WORKDIR/r_library'
Rscript install.R