Run R Script on Linux with Crontab


Recently the in-house server in our company crashed several times because of the heavy duty, so we finally decide to move important cronjobs to AWS. Running java on linux is easy, but for R it’s a little different.

Run R script on Linux with cron tab

  1. Install r on linux:
    • add deb trusty/ and deb https://<my.favorite.ubuntu.mirror>/ trusty-backports main restricted universe to /etc/apt/sources.list file
    • $sudo apt-key adv --keyserver --recv-keys E084DAB9
    • $sudo apt-get update
    • $sudo apt-get install r-base
    • $sudo apt-get install r-base-dev
  2. Use crontab to run scheduled task:
    • Put your own r script under a folder, e.g. /ect/rcronjob/test.R
    • Creat a file under the same file, with content,
       #! /bin/bash
       Rscript /etc/rcronjob/test.R
    • Grand execution to .sh file by
       sudo chmod +x
    • Using crontab
       sudo crontab -e
    • add “* * * * * /etc/rcronjob/”
  3. format: “crontab [-u user] file crontab [-u user] [-e|-l|-r]”
    • -e: edit crontab task list
    • -l: show content
    • input format: min hour day month week commmand
    • example: * * * * * /etc/rcronjob/
    • Example: Rscript /etc/rcronjob/systime.R > /etc/rcronjob/outputFile.txt 2 > /etc/rcronjob/errorFile.txt
  4. Edit crontab file:
    • use vi editor to add/delete cron job
    • Press I to enter insert mode
    • Use ‘ESC’ to quit edit mode, input : to enter commandline mode.
    • q! quit without saving
    • wq save and quit