RMarkdown documents containing params with !r do not render

[fkohrt]

I have:

• searched the issue tracker for similar issues
• installed the latest version of Quarto CLI
• formatted my issue following the Bug Reports guide

Bug description

The documentation at help(topic = "knit_params", package = "knitr") contains the following example document to show how parameters can be populated using R code.

Steps to reproduce

---
title: My Document
output: html_document
params:
  start: !r Sys.Date()
---

Actual behavior

Rendering this document with Quarto leads to the following error:

ERROR: Error reading metadata from quarto-test.Rmd.
unknown tag !<!r> (5:23)

 2 | title: My Document
 3 | output: html_document
 4 | params:
 5 |   start: !r Sys.Date()
---------------------------^
Did you try to use a '!' in a YAML string? If so, you need to add explicit quotes to your string.
ERROR: Error reading metadata from quarto-test.Rmd.
unknown tag !<!r> (5:23)

 2 | title: My Document
 3 | output: html_document
 4 | params:
 5 |   start: !r Sys.Date()
---------------------------^
Did you try to use a '!' in a YAML string? If so, you need to add explicit quotes to your string.
ERROR: Error reading metadata from quarto-test.Rmd.
unknown tag !<!r> (5:23)

 2 | title: My Document
 3 | output: html_document
 4 | params:
 5 |   start: !r Sys.Date()
---------------------------^
Did you try to use a '!' in a YAML string? If so, you need to add explicit quotes to your string.
ERROR: YAMLException: unknown tag !<!r> (5:23)

 2 | title: My Document
 3 | output: html_document
 4 | params:
 5 |   start: !r Sys.Date()
---------------------------^
Did you try to use a '!' in a YAML string? If so, you need to add explicit quotes to your string.

Stack trace:
    at generateError1 (/home/[USER]/bin/quarto/bin/quarto.js:18079:12)
    at throwError1 (/home/[USER]/bin/quarto/bin/quarto.js:18082:11)
    at composeNode1 (/home/[USER]/bin/quarto/bin/quarto.js:18982:13)
    at readBlockMapping1 (/home/[USER]/bin/quarto/bin/quarto.js:18735:17)
    at composeNode1 (/home/[USER]/bin/quarto/bin/quarto.js:18925:85)
    at readBlockMapping1 (/home/[USER]/bin/quarto/bin/quarto.js:18735:17)
    at composeNode1 (/home/[USER]/bin/quarto/bin/quarto.js:18925:85)
    at readDocument1 (/home/[USER]/bin/quarto/bin/quarto.js:19055:5)
    at loadDocuments1 (/home/[USER]/bin/quarto/bin/quarto.js:19097:9)
    at load$11 (/home/[USER]/bin/quarto/bin/quarto.js:19115:21)

Expected behavior

The document should render without errors.

Your environment

• OS: Fedora 42

Quarto check output

Quarto 1.7.31
[✓] Checking environment information...
      Quarto cache location: /home/[USER]/.cache/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.85.1: OK
      Deno version 1.46.3: OK
      Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.7.31
      Path: /home/[USER]/bin/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (not installed)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: Installation From Path
      Path: /usr/local/texlive/2024/bin/x86_64-linux
      Version: 2024

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /usr/bin/chromium-browser
      Source: PATH

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.13.3
      Path: /usr/bin/python3
      Jupyter: 5.7.2
      Kernels: ir, python3

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

[✓] Checking R installation...........OK
      Version: 4.5.1
      Path: /usr/lib64/R
      LibPaths:
        - /home/[USER]/R/x86_64-redhat-linux-gnu-library/4.5
        - /usr/local/lib/R/library
        - /usr/lib64/R/library
        - /usr/share/R/library
      knitr: 1.50
      rmarkdown: 2.29

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

[mcanouil]

@fkohrt Please open discussions rather than issues after you checked the documentation.

• https://quarto.org/docs/computations/r.html#chunk-options

The only supported tag by Quarto (knitr) is !expr.

---
title: My Document
format: html
engine: knitr
params:
  test: !expr "Sys.Date()"
---

[fkohrt]

Quarto's documentation says:

You should generally be able to use Quarto to render any existing Rmd document without changes.

Therefore I think a document provided in the documention of {knitr} that does not render with Quarto is a bug.

But good to know that there's an alternative way to achieve this!

[mcanouil]

Thanks for the mention of the documentation.

I'll let @cderv, the knitr expert, take over.

[cderv]

Therefore I think a document provided in the documention of {knitr} that does not render with Quarto is a bug.

Just to clarify, all that knitr allows and does is not expected 💯 to work in Quarto. Yes, Quarto uses knitr as a backend, but Quarto documents the way that knitr is used in its documentation. knitr does not document what Quarto supports or does not support.

So this is not a bug per se. If you dig into knitr documentation, you will find things that won't work the same in Quarto, mainly because Quarto overrides some default knitr behavior. The same way as R Markdown did when using knitr.

You should generally be able to use Quarto to render any existing Rmd document without changes.

Regarding the error you get, this is because Quarto does validate YAML. So it is expected to have valid YAML and !r is not. !expr works because this was added for backward compatibility. !r was not added.

I think this fall under the generally of the sentence.

Note that if you are using --execute-params or -P cli flag, you won't be able to use any !expr. So parameter support and default value is a bit different than in R Markdown.

I'll think again about supporting also !r but I am more leaning about updating our R Markdown and knitr doc toward using !expr

[fkohrt]

Thank you for the elaboration!

I think support in Quarto for !r is in a way more justifiable than for !expr, given that !r a direct feature of knitr, whereas !expr is "only" a feature of the package yaml utilized by knitr.

If you decide to not support it, I'd recommend documenting this in the FAQ for R Markdown Users (or other breaking changes when transitioning from RMarkdown to Quarto, should there are any).

[cderv]

I don't know which one is the more known

• !r which is special knitr handler support, and only working in knitr
• !expr which will work with any R tool using yaml package.

R Markdown ecosystem documents both...

• !expr is here for custom df.print in R Markown: https://bookdown.org/yihui/rmarkdown/html-document.html#custom-fun-dfprint

  • But also for themes at https://bookdown.org/yihui/rmarkdown/output-formats.html

• !r is for parameters https://bookdown.org/yihui/rmarkdown/params-declare.html

• !expr is also documented as support with Quarto: https://quarto.org/docs/computations/r.html#chunk-options
  for backward compatibility with R.

Also, new litedown R Package by Yihui seems to document !expr not !r: https://yihui.org/litedown/#sec:yaml-syntax so maybe this is getting more common.

If you decide to not support it, I'd recommend documenting this in the FAQ for R Markdown Users (or other breaking changes when transitioning from RMarkdown to Quarto, should there are any).

Yes good idea.