Control which version of R is used during quarto render

[JosiahParry]

Description

Question: how can we control which version of R is used during quarto render?

Context:

This is partially related to the discussion possibility to specify renv for quarto render on the Posit Community page.

One part missing from that discussion is how an R version is chosen for quarto render in the presence of an renv.lock file. At the top of an renv.lock file is the R version that was used to generate the lockfile.

{
  "R": {
    "Version": "4.4.0",

}

I am unsure how quarto chooses which version of R to use. For example I have the following versions of R installed

~ ⚡ rt r-vers
  R 4.1.3
  R 4.3.3
  R 4.4.0
  R 4.4.1 (default)
  R 4.5.0-devel

In this case my default version is fine but ideally I would like to choose the exact match if possible.

Looking at the output of

~ ⚡ quarto check knitr
Quarto 1.6.40
[✓] Checking R installation...........OK
      Version: 4.4.1
      Path: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources
      LibPaths:
        - /Users/josiahparry/Library/R/arm64/4.4/library
        - /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
      knitr: 1.48
      rmarkdown: 2.28

[✓] Checking Knitr engine render......OK

quarto only sees the default version of R. How can we change that?

[mcanouil]

You can use the environment variable QUARTO_R to specify the directory where Rscript is.

You can set this in _environment.yml (_quarto.yml is required, even an empty one).

[JosiahParry]

Do you mean that in order for QUARTO_R to be used there needs to be an _environment.yml file?

[mcanouil]

You can use it as a standard environment variable.

_environment.yml (alongside _quarto.yml) allows you to define environment variables on a per Quarto project basis.

The way you want to set this environment variable is completely up to you.

[JosiahParry]

Thanks! That seems to be it! For posterity: https://quarto.org/docs/advanced/environment-vars.html

Would you mind if I used this thread to ask if there is an environment variable for julia as well but isn't documented? Or is that extracted from the Manifest.toml?

[mcanouil]

Yes, it's QUARTO_JULIA.

• quarto-cli/src/execute/julia.ts

  Lines 133 to 139 in d0d6f87

  	const juliaExecOptions: JuliaExecuteOptions = {
  	julia_cmd: Deno.env.get("QUARTO_JULIA") ?? "julia",
  	oneShot: !executeDaemon,
  	supervisor_pid: options.previewServer ? Deno.pid : undefined,
  	...execOptions,
  	};

[mcanouil]

There are probably detection mechanisms in place but I don't know them. The environment variables take precedence over those mechanisms anyway, so kind of a brute force approach.

[cscheid]

PR adding QUARTO_JULIA to https://quarto.org/docs/advanced/environment-vars.html: quarto-dev/quarto-web#1529