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source /usr/local/bin/s3proxy.sh module load anaconda3/2024.06 conda create --name myRenv R=4.3.1 source activate myRenv To install packes like "tidyverse","lubridate","ggplot2", "tmap", "ggmap", "sf", "ggsci", "remotes", "raster", "readxl", "terra" Simply google with the package name and conda as search strings e.g. tidyverse conda You will see instructions to install these packages: conda install r::r-lubridate conda install r::r-tidyverse conda install conda-forge::r-ggplot2 conda install conda-forge::r-tmap conda install conda-forge::r-ggmap conda install conda-forge::r-sf conda install conda-forge::r-ggsci conda install conda-forge::r-remotes conda install conda-forge::r-raster conda install conda-forge::r-readxl conda install conda-forge::r-terra Or simply: conda create --name myRenv r=4.3.1 r-tidyverse r-ggplot2 r-tmap r-ggmap r-sf r-ggsci r-remotes r-raster r-readxl r-terra -c conda-forge Here is a sample pbs script: #!/bin/bash #PBS -m abe #PBS -M XXXX@griffithuni.edu.au #PBS -N MyTest #PBS -q workq #PBS -l select=1:ncpus=1:mem=4gb,walltime=01:00:00 module load anaconda3/2024.06 source activate myRenv module list cd $PBS_O_WORKDIR R CMD BATCH '--args a=1 b=c(2,5,6)' test.R test.out echo "test Done" echo "Done with job" save' <MAIN_CODEmodel1.R ##sleep 22 echo "Done with job" >>>>> R script can start with loading the packages like this: package_names <- c("tidyverse","lubridate","ggplot2", "tmap", "ggmap", "sf", "ggsci", "remotes", "raster", "readxl", "terra") # Loop to load the packages for (package_name in package_names) { if (!requireNamespace(package_name, quietly = TRUE)) { message(paste("Installing and loading", package_name)) install.packages(package_name, dependencies = TRUE) } library(package_name, character.only = TRUE) } <snip> |
Reference
1. http://yusung.blogspot.com.au/2009/01/install-jags-and-rjags-in-fedora.html
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