R Conda Environment

Getting Started

Below is a step-by-step guide to creating and managing your R Conda environments. Feel free to expand on these details or alter this section to suit your specific instructions.

1. Install Miniconda on HPC.
2. Create a new environment for R (renv.yaml under lab directory):

   conda env create -n renv -f renv.yaml

3. Activate your new R environment:

   conda activate renv

4. Install any additional R packages:

   
             conda install -c r r-tidyverse
             # or in R
             install.packages("tidyverse")
           

5. Verify installed packages:

   conda list

Important Considerations on Package Installation and Running Jobs on HPC

• If you execute a command on IDAS R Studio:
  When you install an R package directly in IDAS terminal, the packages by default will be installed under /Home/.conda/envs/YOUR_ENV_NAME (as seen on the RStudio file browser). RStudio will, but HPC will NOT recognize this address.
• If you run a job on Argon HPC CLI:
  When you install a package, they usually get installed at /Users/HAWK_ID/miniconda3/envs/YOUR_ENV_NAME/lib/R/library on YOUR assigned HPC space.
• To make sure both HPC and IDAS R Studio refer to the same installation location, run .libPaths("CONDA_DIRECTORY_RELATIVE_TO_YOUR_ENV/envs/renv/lib/R/library") before requiring libraries.

Troubleshooting Tips