Error rendering documents with `embed-resources: true` in sym-linked directories

[rundel]

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

When rendering a qmd document using embed-resources: true and a full absolute path that involves a sym-linked directory the render fails when attempting to clean up the *_files/ folder because of confusion between the given and normalized paths.

After the render completes we see an error like the following:

quarto render /home/c/cr173/tmp/quarto-bug/test.qmd

processing file: test.qmd
1/2                  
2/2 [unnamed-chunk-1]
output file: test.knit.md

pandoc 
  to: html
  output-file: test.html
  standalone: true
  embed-resources: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  variables: {}
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  
ERROR: Refusing to remove directory /home/vis/cr173/tmp/quarto-bug/test_files that isn't a subdirectory of /home/c/cr173/tmp/quarto-bug

Stack trace:
    at safeRemoveDirSync (file:///opt/quarto-1.8.26/bin/quarto.js:2540:11)
    at file:///opt/quarto-1.8.26/bin/quarto.js:114469:9
    at Array.forEach (<anonymous>)
    at renderCleanup (file:///opt/quarto-1.8.26/bin/quarto.js:114467:23)
    at file:///opt/quarto-1.8.26/bin/quarto.js:115409:44
    at withTiming (file:///opt/quarto-1.8.26/bin/quarto.js:18977:21)
    at Object.complete (file:///opt/quarto-1.8.26/bin/quarto.js:115409:9)
    at eventLoopTick (ext:core/01_core.js:178:7)
    at async Object.onPostProcess (file:///opt/quarto-1.8.26/bin/quarto.js:123992:28)
    at async renderFileInternal (file:///opt/quarto-1.8.26/bin/quarto.js:123976:3)

Note the difference between /home/vis/cr173/tmp/quarto-bug/test_files and /home/c/cr173/tmp/quarto-bug. On our server /home/c/cr173 is a sym-link to /home/vis/cr173.

Myself and @mine-cetinkaya-rundel ran into the issue on our departmental server(s) running Posit Workbench (2026.01.0+392.pro5). It was originally observed when rendering from Positron but we've been able to replicate it with the quarto cli using versions 1.8.25, 1.8.26, and 1.9.16.

Steps to reproduce

Create test.qmd in /data/quarto-bug/:

---
format: 
  html:
    embed-resources: true
---

```{r}
plot(mtcars)
```

Create a symlink from quarto-bug/ to quarto-bug-sym/ in data/.

Run the following from /data/quarto-bug/ or /data/quarto-bug-sym:

• quarto render /data/quarto-bug-sym/test.qmd - fails
• quarto render /data/quarto-bug/test.qmd - succeeds
• quarto render test.qmd - succeeds

Actual behavior

Using a path with a sym-link fails with the above error

Expected behavior

Sym-link path should be normalized to avoid the error

Your environment

• IDE: Posit Workbench 2026.01.0+392.pro5
• OS: Fedora 43

Quarto check output

Quarto 1.8.26
[✓] Checking environment information...
      Quarto cache location: /home/c/cr173/.cache/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.87.0: OK
      Deno version 2.3.1: OK
      Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.8.26
      Path: /opt/quarto-1.8.26/bin

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

[✓] Checking LaTeX....................OK
      Using: Installation From Path
      Path: /usr/bin
      Version: 2023

[✓] Checking Chrome Headless....................OK
      Chrome:  (not detected)

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

[✓] Checking Python 3 installation....OK
      Version: 3.14.2
      Path: /usr/bin/python3
      Jupyter: 5.8.1
      Kernels: python3

(/) Checking Jupyter engine render....[IPKernelApp] WARNING | debugpy_stream undefined, debugging will not be enabled
[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.5.2
      Path: /usr/lib64/R
      LibPaths:
        - /home/vis/cr173/R/x86_64-redhat-linux-gnu-library/4.5
        - /usr/local/lib/R/library
        - /usr/lib64/R/library
        - /usr/share/R/library
      knitr: 1.51
      rmarkdown: 2.30

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

[cderv]

I have a possible fix for this. It is hard to test and be sure of side effect but I think it will work and be better.

My understanding is that some codepath in quarto does not resolve symlink, but inside knitr we do, and this leads to the problem.

Anyhow, I added a test that seems to be passing.

This runs: https://github.com/quarto-dev/quarto-cli/actions/runs/21040508847 will have artifact for a quarto binary you could try out. Unless you are on MAC because we have a mac signing problem for now.

If you are able to try that would be awesome !

[rundel]

I didnt get a chance to test this yet, on that actions page I am only seeing mac artifacts and not any of the linux artifacts - ami I missing something obvious?

[cderv]

Nope there is a problem... I'll retrigger a build: https://github.com/quarto-dev/quarto-cli/actions/runs/21061352514

Also, I am having second thoughts on the way to solve this. Basically, this happens because knitr will resolve symlink while quarto does not. So when comparing path for deletion, this is a problem.

I targeted something at the quarto level, but I wonder if we should solve this at the R code level to ensure the resource directory for *_files folder is not a resolved symlink

[rundel]

I've just tested the new build on our server and can confirm that the issue is fixed when using knitr & the sym-linked directory.

I also just tested the old and new build using the jupyter engine and I don't see an issue in either case.