CODEWITHSUNDEEP
rcronr-markdownpandocrstudio-server
Mark Heckmann
Mark Heckmann

Reputation: 11441

pandoc from RSudio Server not recognized when running script via cron

On a server, I want cron to run an R script which renders an HTML page using rmarkdown. RStudio server is installed. The crontab entry for user mark is:

* * * * * Rscript R/test.R >> /tmp/cron.log 2>&1

test.R:

library(rmarkdown)
getwd()
render("R/test.Rmd")

The cron.log file shows

[1] "/home/mark"
Error: pandoc version 1.12.3 or higher is required and was not found.
Execution stopped

Running test.R from the console, however, works fine:

Rscript R/test.R

The RStudio server version of pandoc was added to usr/local/bin using a symlink as described here). Checking the pandoc version in the console gives

mark@myserver:$ pandoc -v
pandoc 1.15.2

which is not the old version as in the log file. Also, the binary appears to be found 

mark@myserver:$ which pandoc
/usr/local/bin/pandoc

I am not sure what is going on. Any ideas?

Upvotes: 2

Views: 1655

Answers (1)

Jonathan
Jonathan

Reputation: 8812

It's likely that /usr/local/bin is being added to your $PATH in your bash shell, but that your cron job is not running under bash and so doesn't have pandoc on the path. To test this assumption, add these lines to your R file:

Sys.getenv("PATH")
Sys.which("pandoc")

If that's indeed the case, you could have your R script append to $PATH as appropriate, or have cron run the job under a bash shell.

If all else fails, you could set RSTUDIO_PANDOC: 

Sys.setenv(RSTUDIO_PANDOC = "/usr/local/bin/pandoc")

Upvotes: 5

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