How to schedule a R script in YAML file to run daily via Bitbucket Pipelines?

[aqsmith08]

Let's pretend I have a R script called foo.R that outputs a CSV file. I'd like to schedule foo.R to run 1x per day. I found that I should create a YAML file and then schedule it via the Bitbucket GUI per this article.

My YAML file looks like this:

pipelines:
 custom:
 foo-pipeline: # The name displayed in the Bitbucket Cloud GUI
 - step:
 script:
 - echo "Starting Bitbucket Pipeline!"
 - sudo Rscript -e "/file/path/to/foo.R"
 - echo "Bitbucket Pipeline complete!"

That receives and error with this message -- sudo: Rscript: command not found.

I'm not sure how to figure this out and would love advice. Thanks!

[aqsmith08 · Accepted solution]

Thanks to Gonchik and some investigation, I figured this out. The YAML looks like this --

image: rocker/tidyverse

pipelines:
  custom:
    foo-pipeline: # The name displayed in the Bitbucket Cloud GUI
      - step:
          script:
            - Rscript "file/path/to/foo.R"
            - git add "file/path/to/foo.csv"
            - git commit -m "[Pipeline] Add foo CSV file."
            - git push

Works great and automatically pushes the CSV file into the repo I'm working in. 

[Gonchik Tsymzhitov]

Hi! 

Have you determine the your Docker image with rscript?

https://confluence.atlassian.com/bitbucket/get-started-with-bitbucket-pipelines-792298921.html

https://confluence.atlassian.com/bitbucket/use-docker-images-as-build-environments-792298897.html

Cheers,

Gonchik Tsymzhitov

[aqsmith08]

At first, I mistakenly thought I could use the Default but that's not the case since it doesn't include R. I'll try using the rocker/tidyverse one and see if that does the trick.

[Gonchik Tsymzhitov]

Good :)