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Friday, 3 July 2015

Batch processing & scheduling of R



Scheduling R script runs in Windows

1. create a batch file (.bat) with the below command

"Your path to R.exe (e.g. C:\Program Files\R-2.12.0\bin\x64\R.exe)" CMD BATCH "Your path to script file (e.g. C:\Documents\Rscript.r)"

2. Use Windows Task Scheduler to create trigger pointing to the batch file created above.



NOTE:

If the script has any dependency on the log-in credentials or if the script accesses folders requiring specific permissions, selecting the option 'Run whether user is logged on or not' may generate access denied errors.




Scheduling R script runs in Linux

There are several options, but one simple option is to use Crontab


http://www.adminschoice.com/crontab-quick-reference


e.g.

The following will run r script at 6.30 PM everyday

30     18     *     *     *        Rscript /home/your path/rscriptfile.r



If this is running from a server and if it should run regardless of whether user is logged in or not (i.e. run in the background or run as a root) disown the process as below

30     18     *     *     *        Rscript /home/your path/rscriptfile.r & disown  


If you are connecting to a database inside the R script, you may need to export the environment for the database used when you run the R script. Alternatively, you may save the environment in your bash_profile and call it before R script is run.

30     18     *     *     *        source ~/.bash_profile && Rscript /home/your path/rscriptfile.r & disown  



The above example used && as the R script is dependent on the successful set up of the database environment. If you are running scripts consecutively, independent of the outputs of each other, you may use ; (semicolon) instead of &&.


30     18     *     *     *       Rscript /home/your path/rscriptfile1.r;  Rscript /home/your path/rscriptfile2.r   






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