Bug when building a PDF document containing Mermaid graph using Gitlab CI

[barriern]

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

Hi everyone.

When I try to build a PDF document from Quarto files containing Mermaid graphs, I encounter an issue.

The error messages are as follows:

[✓] Checking Julia installation...
build-pages $ export QUARTO_PRINT_STACK=true
build-pages $ quarto render doc --output-dir=public
[1/3] index.qmd
[2/3] developer.qmd
[3/3] developer/manager_initialization.qmd
build-pages > ERROR: AssertionError: 
build-pages > 
build-pages > Stack trace:
build-pages >     at assert (file:///opt/quarto/bin/quarto.js:470:11)
build-pages >     at assert7 (file:///opt/quarto/bin/quarto.js:68259:3)
build-pages >     at criClient (file:///opt/quarto/bin/quarto.js:68348:7)
build-pages >     at eventLoopTick (ext:core/01_core.js:218:9)
build-pages >     at async file:///opt/quarto/bin/quarto.js:68296:16
build-pages >     at async Semaphore.runExclusive (file:///opt/quarto/bin/quarto.js:67644:27)
build-pages >     at async Object.createPngsFromHtml (file:///opt/quarto/bin/quarto.js:68620:36)
build-pages >     at async Object.cell (file:///opt/quarto/bin/quarto.js:132394:11)
build-pages >     at async Promise.all (index 0)
build-pages >     at async Object.document (file:///opt/quarto/bin/quarto.js:69029:25)
build-pages >     at async handleLanguageCells (file:///opt/quarto/bin/quarto.js:68829:34)
build-pages >     at async file:///opt/quarto/bin/quarto.js:136718:41
build-pages >     at async withTimingAsync (file:///opt/quarto/bin/quarto.js:15978:21)
build-pages >     at async renderFileInternal (file:///opt/quarto/bin/quarto.js:136717:9)
build-pages >     at async renderFiles (file:///opt/quarto/bin/quarto.js:136483:9)
build-pages >     at async renderProject (file:///opt/quarto/bin/quarto.js:137052:23)
build-pages >     at async _Command.actionHandler (file:///opt/quarto/bin/quarto.js:142382:24)
build-pages >     at async _Command.execute (file:///opt/quarto/bin/quarto.js:102005:7)
build-pages >     at async _Command.parseCommand (file:///opt/quarto/bin/quarto.js:101882:14)
build-pages >     at async quarto4 (file:///opt/quarto/bin/quarto.js:187491:5)
build-pages >     at async file:///opt/quarto/bin/quarto.js:187519:5
build-pages >     at async file:///opt/quarto/bin/quarto.js:187374:14
build-pages >     at async mainRunner (file:///opt/quarto/bin/quarto.js:187376:5)
build-pages >     at async file:///opt/quarto/bin/quarto.js:187512:3
build-pages > Error occurred during cleanup: TypeError: Child process has already terminated
build-pages finished in 19 s  FAIL 1 

 FAIL  build-pages
  >     at async mainRunner (file:///opt/quarto/bin/quarto.js:187376:5)
  >     at async file:///opt/quarto/bin/quarto.js:187512:3
  > Error occurred during cleanup: TypeError: Child process has already terminated
pipeline finished in 19 s

If I remove any reference to Mermaid it works. And if I build only the HTML without the PDF it works too. This issue was tested on the following simple project: https://forge.ird.fr/marbec/ichthyop/test-gitlab-ichthyop

Log messages are here: https://forge.ird.fr/marbec/ichthyop/test-gitlab-ichthyop/-/jobs/246132

Thanks for your help

Nicolas

Steps to reproduce

You can clone the repository:

git clone https://forge.ird.fr/marbec/ichthyop/test-gitlab-ichthyop.git

And on Linux, you can simply download the gitlab-local-ci tool and run, within the proper folder:

gitlab-ci-local

Actual behavior

No response

Expected behavior

No response

Your environment

No response

Quarto check output

The quarto check command returns:

build-pages $ quarto check
build-pages > Quarto 1.9.29
[✓] Checking environment information...
build-pages >       Quarto cache location: /root/.cache/quarto
[✓] Checking versions of quarto binary dependencies...
build-pages >       Pandoc version 3.8.3: OK
build-pages >       Dart Sass version 1.87.0: OK
build-pages >       Deno version 2.4.5: OK
build-pages >       Typst version 0.14.2: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
build-pages >       Version: 1.9.29
build-pages >       Path: /opt/quarto/bin
build-pages > 
[✓] Checking tools....................OK
build-pages >       TinyTeX: (external install)
build-pages >       Chrome Headless Shell: 146.0.7680.66
build-pages >       Chromium: (not installed)
build-pages >       VeraPDF: (not installed)
build-pages > 
[✓] Checking LaTeX....................OK
build-pages >       Using: Installation From Path
build-pages >       Path: /usr/local/bin
build-pages >       Version: 2026
build-pages > 
[✓] Checking Chrome Headless....................OK
build-pages >       Using: Chrome Headless Shell installed by Quarto
build-pages >       Path: /root/.local/share/quarto/chrome-headless-shell/chrome-headless-shell-linux64/chrome-headless-shell
build-pages >       Version: 146.0.7680.66
build-pages > 
[✓] Checking basic markdown render....OK
build-pages > 
[✓] Checking R installation...........OK
build-pages >       Version: 4.3.3
build-pages >       Path: /opt/R/4.3.3/lib/R
build-pages >       LibPaths:
build-pages >         - /opt/R/4.3.3/lib/R/library
build-pages >       knitr: (None)
build-pages >       rmarkdown: (None)
build-pages > 
build-pages >       The knitr package is not available in this R installation.
build-pages >       Install with install.packages("knitr")
build-pages >       The rmarkdown package is not available in this R installation.
build-pages >       Install with install.packages("rmarkdown")
build-pages > 
[✓] Checking Python 3 installation....(None)
build-pages > 
build-pages >       Unable to locate an installed version of Python 3.
build-pages >       Install Python 3 from https://www.python.org/downloads/
build-pages > 
[✓] Checking Julia installation...

[mcanouil]

Have you tried your workflow locally using the same dependencies, especially the headless chrome?

You are mentioning mermaid, but you don't have mermaid diagram in your repository.

[mcanouil]

Where did you see that pdf was a valid value for mermaid-format?

• https://quarto.org/docs/authoring/diagrams.html#mermaid-formats

For PDF format, png is enforced and mermaid-format from user is ignored.

[barriern]

The bug I have is with Mermaid, so I tested with GraphViz (this is what is in my repo). But there is the same issue with both Mermaid and GraphViz.

If I try locally without using Gitlab CI or the docker image, it works.

[mcanouil]

The bug I have is with Mermaid, so I tested with GraphViz (this is what is in my repo). But there is the same issue with both Mermaid and GraphViz.

When sharing code, it's better to keep it consistent with the issue being reported.
Could you simplify your example using a single document instead of a book and see if it works?

If I try locally without using Gitlab CI or the docker image, it works.

Using the same Chrome Headless Shell 146.0.7680.66?

[mcanouil]

Here is a mimimal reproducible example that does not require a book project nor to use GitLab:

docker run -it --platform linux/amd64 --rm ghcr.io/quarto-dev/quarto-full:1.9.29 bash -lc "cat > document.qmd <<'EOF'
---
format: pdf
---

\`\`\`{dot}
graph G {
  layout=neato
  run -- intr;
}
\`\`\`
EOF
quarto install chrome-headless-shell --no-prompt
export QUARTO_PRINT_STACK=true
export QUARTO_LOG_LEVEL=DEBUG
quarto render document.qmd"

Installing chrome-headless-shell
[✓] Downloading Chrome Headless Shell
Installation successful
Quarto version: 1.9.29
[CHROMIUM] Using Chrome Headless Shell installed by Quarto: /root/.local/share/quarto/chrome-headless-shell/chrome-headless-shell-linux64/chrome-headless-shell
[CHROMIUM path]   : /root/.local/share/quarto/chrome-headless-shell/chrome-headless-shell-linux64/chrome-headless-shell
[CHROMIUM cmd]   : [object Object]
[NotebookContext]: Starting Cleanup
ERROR: AssertionError: 

Stack trace:
    at assert (file:///opt/quarto/bin/quarto.js:470:11)
    at assert7 (file:///opt/quarto/bin/quarto.js:68259:3)
    at criClient (file:///opt/quarto/bin/quarto.js:68348:7)
    at eventLoopTick (ext:core/01_core.js:218:9)
    at async file:///opt/quarto/bin/quarto.js:68296:16
    at async Semaphore.runExclusive (file:///opt/quarto/bin/quarto.js:67644:27)
    at async Object.createPngsFromHtml (file:///opt/quarto/bin/quarto.js:68620:36)
    at async Object.cell (file:///opt/quarto/bin/quarto.js:132394:11)
    at async Promise.all (index 0)
    at async Object.document (file:///opt/quarto/bin/quarto.js:69029:25)
    at async handleLanguageCells (file:///opt/quarto/bin/quarto.js:68829:34)
    at async file:///opt/quarto/bin/quarto.js:136718:41
    at async withTimingAsync (file:///opt/quarto/bin/quarto.js:15978:21)
    at async renderFileInternal (file:///opt/quarto/bin/quarto.js:136717:9)
    at async renderFiles (file:///opt/quarto/bin/quarto.js:136483:9)
    at async render (file:///opt/quarto/bin/quarto.js:142137:19)
    at async _Command.actionHandler (file:///opt/quarto/bin/quarto.js:142382:24)
    at async _Command.execute (file:///opt/quarto/bin/quarto.js:102005:7)
    at async _Command.parseCommand (file:///opt/quarto/bin/quarto.js:101882:14)
    at async quarto4 (file:///opt/quarto/bin/quarto.js:187491:5)
    at async file:///opt/quarto/bin/quarto.js:187519:5
    at async file:///opt/quarto/bin/quarto.js:187374:14
    at async mainRunner (file:///opt/quarto/bin/quarto.js:187376:5)
    at async file:///opt/quarto/bin/quarto.js:187512:3

[barriern]

Thanks for the reproducible exemple. For the record, on my local system (where the code works), the quarto check command returns:

Quarto 1.8.27
[✓] Checking environment information...
      Quarto cache location: /home/BARRIER/.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: 1.8.27
      Path: /opt/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: v2025.10
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /home/BARRIER/.TinyTeX/bin/x86_64-linux
      Version: 2025

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

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

[✓] Checking Python 3 installation....OK
      Version: 3.10.12
      Path: /usr/bin/python3
      Jupyter: 5.3.1
      Kernels: python3

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

[✓] Checking R installation...........OK
      Version: 4.5.2
      Path: /usr/lib/R
      LibPaths:
        - /home/BARRIER/R/x86_64-pc-linux-gnu-library/4.5
        - /usr/local/lib/R/site-library
        - /usr/lib/R/site-library
        - /usr/lib/R/library
      knitr: (None)
      rmarkdown: (None)

      The knitr package is not available in this R installation.
      Install with install.packages("knitr")
      The rmarkdown package is not available in this R installation.
      Install with install.packages("rmarkdown")

Best, Nicolas