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/tmp No space left on device / Error: Fatal error: cannot create 'R_TempDir'

Explanation

The server on which the job ran must have a full on its /tmp/. Indeed, by default, R by default, is writing temporary files in the /tmp/ directory of the server.

The local directory /tmp/ is limited and shared. It's not a good practice to let a software writing on local disk.

Solution

The solution is to change the default temporary directory and expect that the tool is well developed (and the /tmp not hard-coded).

Please add the following lines at the beginning of your sbatch script.

#!/bin/bash
# SBATCH -p fast

TMPDIR="/shared/projects/my_intereting_project/tmp/"
TMP="${TMPDIR}"
TEMP="${TMPDIR}"
mkdir -p "${TMPDIR}"
export TMPDIR TMP TEMP

module load r/4.1.1
Rscript my_script.R