cannot get a r markdown to run with cronR

[aayushsahni]

Please ask your questions about R Markdown here.

Unable to execute my r markdown file when running via a cronR job

My code errors out at this line. Has anyone see this before, I tried to google this but to no good use.

rmarkdown::render("markdowns/xyz/xyz/xyz.Rmd",params=params,output_file="xyz/xyz_results.HTML",output_format = "html_document")

while executing a cronR job.

[andresrcs]

What is the error message you are getting? Have in mind that a cron job doesn't run on the same working directory that you where when you wrote the script.

[aayushsahni]

Hi,

Thank you for the prompt reply!

Yes, I took the change in directory into account. It still errors out

Best,
Aayush Sahni

[andresrcs]

Ok, but what the error message says?

[aayushsahni]

Hi Andrés,

Please find below the error message:
Error: pandoc version 1.12.3 or higher is required and was not found.
Execution stopped

I have checked the Rstudio pandoc version and I have 1.19.2.1. Is there a difference between running the job from RStudio terminal and Putty

Best,
Aayush Sahni

[andresrcs]

Try manually setting the location of pandoc in your script

Sys.setenv(RSTUDIO_PANDOC="/usr/lib/rstudio-server/bin/pandoc")

[aayushsahni]

Thank you! I asked my backend team to add pandoc to my r-server bin as well. Solved the issue