Can't change "output_dir" in the YAML metadata

[thombet]

Checklist

When filing a bug report, please check the boxes below to confirm that you have provided us with the information we need. Have you:

• formatted your issue so it is easier for us to read?

• included a minimal, self-contained, and reproducible example?

• pasted the output from xfun::session_info('rmarkdown') in your issue?

• upgraded all your packages to their latest versions (including your versions of R, the RStudio IDE, and relevant R packages)? I use RMarkdown 2.29 and I cannot upgrade to the latest version (2.31) currently but reading the release notes of versions 2.30 and 2.31, I think the issue was not fixed in these newer versions.

• installed and tested your bug with the development version of the rmarkdown package using remotes::install_github("rstudio/rmarkdown") ? Same as above.

Bug description

Hello,

I am not able to change the output directory of an HTML document using the examples provided here and here.

Here is the content of a test.Rmd file:

---
title: "Test"
output: html_document
knit: (function(input, ...) {
    rmarkdown::render(
      input,
      output_dir = "docs/html"
    )
  })
---

This is a test document.

```{r dummy-chunk}
sample(letters, 2)
```

When I call in the R terminal

rmarkdown::render("test.Rmd")

the file test.html is generated in the same folder as test.Rmd whereas I would have expected it to be located in the folders docs/html.

Setting explicitly the output_dir in the command works as expected though:

rmarkdown::render("test.Rmd", output_dir = "docs/html")

Is this a bug or am I using the knit arguments in the metadata in the wrong way?

Thanks in advance for your help.

Session information

xfun::session_info('rmarkdown')

R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS, RStudio 0

Locale:
  LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=fr_FR.UTF-8   
  LC_MESSAGES=en_GB.UTF-8    LC_PAPER=fr_FR.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
  LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

Package version:
  base64enc_0.1.3   bslib_0.9.0       cachem_1.1.0      cli_3.6.5         digest_0.6.37     evaluate_1.0.4    fastmap_1.2.0     fontawesome_0.5.3
  fs_1.6.6          glue_1.8.0        graphics_4.5.1    grDevices_4.5.1   highr_0.11        htmltools_0.5.8.1 jquerylib_0.1.4   jsonlite_2.0.0   
  knitr_1.50        lifecycle_1.0.4   memoise_2.0.1     methods_4.5.1     mime_0.13         R6_2.6.1          rappdirs_0.3.3    rlang_1.1.7      
  rmarkdown_2.29    sass_0.4.10       stats_4.5.1       tinytex_0.57      tools_4.5.1       utils_4.5.1       xfun_0.52         yaml_2.3.10      

Pandoc version: 3.6.2