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).

[mcanouil]

I did some tests and with/without a direct path to Rscript, all works, including symbolic link: (@cderv fixed this actually in 1.4, which I forgot about)

❯ QUARTO_R=/usr/local/bin/Rscript quarto render index.qmd



- The project is out-of-sync -- use `renv::status()` for details.
ℹ R version 4.4.2 (2024-10-31)
! Config '~/.Rprofile' was loaded!


processing file: index.qmd
output file: index.knit.md

pandoc 
  to: html
  output-file: index.html
  standalone: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  title: Quarto Playground
  
Output created: index.html

❯ QUARTO_R=/usr/local/bin quarto render index.qmd



- The project is out-of-sync -- use `renv::status()` for details.
ℹ R version 4.4.2 (2024-10-31)
! Config '~/.Rprofile' was loaded!


processing file: index.qmd
output file: index.knit.md

pandoc 
  to: html
  output-file: index.html
  standalone: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  title: Quarto Playground
  
Output created: index.html

❯ ln -s /usr/local/bin/Rscript Rscript
    ~/Projects/quarto/quarto-playground 
❯ QUARTO_R=/Users/mcanouil/Projects/quarto/quarto-playground/Rscript quarto render index.qmd


- The project is out-of-sync -- use `renv::status()` for details.
ℹ R version 4.4.2 (2024-10-31)
! Config '~/.Rprofile' was loaded!


processing file: index.qmd
output file: index.knit.md

pandoc 
  to: html
  output-file: index.html
  standalone: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  title: Quarto Playground
  
Output created: index.html

[mcanouil]

I've tried using /R /Rscript, /RScript, and /Resources as well.

R is installed using rig. There are no symlinks except for Current

drwxr-xr-x@  7 root  admin   224B Jun 27  2024 4.1-arm64
drwxr-xr-x@  8 root  admin   256B Apr 13  2024 4.3-arm64
drwxr-xr-x@  8 root  admin   256B Jan 23 09:00 4.4-arm64
drwxr-xr-x@  7 root  admin   224B Jun 25  2024 4.5-arm64
lrwxrwxr-x   1 root  admin     9B Apr 13  2024 Current -> 4.4-arm64

Ok, let me try with a similar setup.

[mcanouil]

I cannot reproduce either.

To illustrate with an obvious wrong path:

[mcanouil]

@JosiahParry are you sure the error is not coming from env -i QUARTO_R=/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/Rscript rather than Quarto?

env: quarto: No such file or directory

The error is prefixed env.

I think that's the issue

Try with full path to Quarto:

env -i /opt/quarto/bin/quarto --version
1.6.40

[JosiahParry]

Ah! 🤦🏻‍♂️ Yes! So sorry. because it gets rid of PATH which is where quarto is being called from.