.Rprofile not invoked under cron

Question

I am running Ubuntu 16.04.3 LTS on the cloud. When I run a program from the command line with Rscript everything goes as expected. However, when I run the same program with Rscript through cron it appears that my .Rprofile file is not invoked. I have written a small program to demonstrate this problem:

test_cron = function() {
    #The next 3 lines are base R.
    sink('~/test_cron.out')
    on.exit(sink())
    cat('The date and time are:', as.character(Sys.time()), '\n')
    #Now try to access a personal option, set by .Rprofile.
    root = getOption('root')
    cat('Option root:', root, '\n')
}
test_cron()

I run this from the command line using this command:

Rscript test_cron.r

The cron_test.out file contains the following:

The date and time are: 2017-11-14 06:15:46
Option root: /home/ubuntu/_algi/

The relevant line in crontab is as follows:

20 6 * * * /usr/bin/Rscript ~/test_cron.r

When this is run by cron, cron_test.out contains the following:

The date and time are: 2017-11-14 06:20:01
Option root:

Evidently the program, when run by cron, could not access my personal option 'root'. This is one among a number of experiments I have run that convince me that .Rprofile is not invoked under cron. Is there a fix for this?

Note: The R_PROFILE_USER environment variable is set to point to my .Rprofile file. Apparently, Rscript under cron ignores it.

score 2 · Answer 1 · answered Nov 14 '17 at 08:00

By default R looks for and runs .Rprofile files in the three locations in a specific order which are:

R_HOME: the directory in which R is installed
HOME: the user’s home directory
R’s current working directory

.Rprofile in you current project/wd will override .Rprofile in HOME and R_HOME and .Rprofile in HOME will override R_HOME.

So to to create a project-specific start-up script, simply create a .Rprofile file in the project’s root directory.

It looks like in your case that R uses a different .Rprofile file when a script is started by cron than starting a script from the command line.

I edited my question to note that I have the R_PROFILE_USER environment variable set to point to my .Rprofile file. Presumably Rscript under cron is ignoring this. In any event, your answer, while of pedagogical interest, does not provide a fix for the problem, or if it does I don't see it. — Argent, Nov 14 '17 at 08:06

score 0 · Answer 2 · answered Nov 15 '17 at 01:20

It transpires that cron does not load the user's environment. This has caused endless confusion and anguish, with no commonly accepted solution. See, for example,

https://serverfault.com/questions/673480/load-users-environment-variables-in-a-cronjob
https://stackoverflow.com/questions/15557777/cron-job-does-not-get-the-environment-variables-set-in-bashrc
https://stackoverflow.com/questions/2229825/where-can-i-set-environment-variables-that-crontab-will-use
https://unix.stackexchange.com/questions/27289/how-can-i-run-a-cron-command-with-existing-environmental-variables

A closely related problem is that .bashrc will only run in an interactive shell::

https://unix.stackexchange.com/questions/257571/why-does-bashrc-check-whether-the-current-shell-is-interactive

My solution is to write a shell script in which I set the necessary environment variables, then run my program:

#!/bin/bash
export CODE_HOME='/home/ubuntu/'
export OS='Ubuntu'
export R_PROFILE_USER=~/R/.Rprofile
/usr/bin/Rscript ~/test_cron.r

After making the script executable, it successfully runs under crontab.

.Rprofile not invoked under cron

2 Answers2