How to run an R script in crontab

Question

Using crontab -e I've tried:

* * * * *  Rscript /home/.../file.r
* * * * * /usr/lib/R/bin/Rscript /home/.../file.r
* * * * * /usr/bin/Rscript /home/.../file.r
* * * * * /home/.../foo.sh

where foo.sh contains:

sudo R CMD BATCH file.r

Just running $ ./foo.sh works. $ R CMD BATCH file.r works.

Nothing I've tried in crontab works. Any ideas?

Answer 1

You'll need to have the full path in your foo.sh:

sudo R CMD BATCH /home/.../file.r

I should also add that the first version worked for me, although I set it to a specific time rather than * * * * *

Answer 2

For what it is worth here is CRANberries entry which has worked (multiple times) every day for 5+ years:

# every few hours, run cranberries
11 */2 * * *    edd     ~/cranberries/cranberries.r

Of note here are

1. The time specification, here 11 mins past the hour every two hours
2. The user
3. The complete path, using 'globbing' to expand ~ to $HOME for edd

and after that you just have to make sure the script is actually executable. Whether you use Rscript, littler or R BATCH CMD does not matter.

Answer 3

in my user level crontab I run a R script to collect tweets from various sources.

I used: crontab -u myusername -e added this to the end of my crontab file

0 0 * * * /home/bob/Documents/SWtweets/tweetbash.sh

I ran it as a user vs root, don't what difference it makes, but it only worked for me when I ran it at user level.

below is what I put in my tweetbash.sh shell script, which tells the bash program to run the R script located at the path indicated.

#! /bin/bash R CMD BATCH /home/bob/Documents/SWtweets/tweets.R

did chmod +x tweetbash.sh

it works for my purposes.

Bob