Flakiness with include and nested code blocks

[aoanla]

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

There's some weird flakiness with {{< include >}} and nested code blocks, which I can't find a simple reproducer for.

In a fairly complex document, I have the setup

index.qmd
-has the header info and some introductory content
{{< include L2_3.qmd >}}

L2_3.qmd
- has a lot more content, including nested callouts, some of which also include syntax highlighted code blocks (but not executed code because that doesn't work inside callouts)

quarto preview can happily render HTML previews of L2_3.qmd by itself, correctly rendering the nested callouts and code blocks.

However, if I try to to use quarto preview to render an HTML preview of index.qmd, it fails when it tries to parse the include, with the error:

FATAL (/opt/quarto-1.8.27/share/filters/main.lua:4423) An error occurred:
Found a nested callout in the document. Please fix this issue and try again.
Error running filter /opt/quarto-1.8.27/share/filters/main.lua:
/opt/quarto-1.8.27/share/filters/main.lua:1213: FATAL QUARTO ERROR
stack traceback:
/opt/quarto-1.8.27/share/filters/main.lua:2619: in function 'fatal'
/opt/quarto-1.8.27/share/filters/main.lua:2199: in function 'fail'
/opt/quarto-1.8.27/share/filters/main.lua:4423: in function </opt/quarto-1.8.27/share/filters/main.lua:4336>
(...tail calls...)
/opt/quarto-1.8.27/share/filters/main.lua:1213: in local 'filter_fn'
/opt/quarto-1.8.27/share/filters/main.lua:653: in function </opt/quarto-1.8.27/share/filters/main.lua:643>
(...tail calls...)
....8.27/share/pandoc/datadir/../../filters/modules/jog.lua:34: in upvalue 'run_filter_function'
....8.27/share/pandoc/datadir/../../filters/modules/jog.lua:223: in function <....8.27/share/pandoc/datadir/../../filters/modules/jog.lua:202>
(...tail calls...)
[C]: in function 'pandoc.List.map'
....8.27/share/pandoc/datadir/../../filters/modules/jog.lua:125: in upvalue 'recurse'
....8.27/share/pandoc/datadir/../../filters/modules/jog.lua:222: in local 'jogger'
....8.27/share/pandoc/datadir/../../filters/modules/jog.lua:171: in upvalue 'recurse'
....8.27/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <....8.27/share/pandoc/datadir/../../filters/modules/jog.lua:202>
(...tail calls...)
/opt/quarto-1.8.27/share/filters/main.lua:572: in function </opt/quarto-1.8.27/share/filters/main.lua:550>
(...tail calls...)
/opt/quarto-1.8.27/share/filters/main.lua:1314: in local 'callback'
/opt/quarto-1.8.27/share/filters/main.lua:1332: in upvalue 'run_emulated_filter_chain'
/opt/quarto-1.8.27/share/filters/main.lua:1368: in function </opt/quarto-1.8.27/share/filters/main.lua:1365>
WARN: Error encountered when rendering files

Now, this error isn't very helpful - nested callouts do work, so I'm not sure how I'm supposed to "fix" the problem that suddenly they fail in imported documents.

I've tried to reproduce this with chunks of the included document - including parts with the most complex nesting of callouts and syntax highlighted code blocks - and I can't get it to fail in the same way.

Steps to reproduce

I don't know how to reproduce this bug in a minimal way.

Actual behavior

No response

Expected behavior

No response

Your environment

Fedora 42
VSCodium
Quarto 1.8.27

Quarto check output

Quarto 1.8.27
[✓] Checking environment information...
Quarto cache location: /home/aoanla/.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-1.8.27/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: 3.13.11
Path: /home/aoanla/P2T2026/.venv/bin/python
Jupyter: 5.9.1
Kernels: python3, julia-1.11, julia-1.12

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

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

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

[aoanla]

Aha, I've found the reproducer - I never expected it to be the document type.

Any trivial included document with nested code blocks will cause quarto preview to break

if:

the project type is "website".

They do not break if the project type is "manuscript".

So, this is a bug with however quarto builds websites with include.

[mcanouil]

Could you properly format your post using code blocks for code and terminal outputs? Thanks.
If your code contains code blocks, you need to enclose it using more backticks, i.e., usually four ````.
See https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us.

[mcanouil]

@aoanla You need to provide a reproducible example. With only snippet of codes and no concrete examples, the team cannot guess what is needed to reproduce and as time is a major constraint, if you want help, you need to help us first by providing such example.

Also, taking the time to properly format your issue help future readers to read and understand faster.

Thank you for your understanding.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code block (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.

[mcanouil]

Finally, note the error message:

Found a nested callout in the document. Please fix this issue and try again.

Quarto is telling you what is the issue.
With the information provided, the only "bug" is the stack trace being displayed to users.

[aoanla]

hi:

You have a reproducible example explained in the comment I made to the main submission.
Just make an almost empty index.qmd with

{{< include other.qmd >}}

in it

an other.qmd with any nested callouts in it

and a _quarto.yml with the project set to website.

In addtion:

Yes, if you read the update, you'll see my observation is that this works for project = manuscript but does not work for project = website.

So, the bug is "nested callouts don't work in website, with included files but do work in maniscript with included files".

I hope this is enough information for you to reproduce the problem.

[mcanouil]

@aoanla Could you please follow the guidelines about sharing examples and formatting your code?
Here are the links again for your convenience:

• https://quarto.org/bug-reports.html
• https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us

[aoanla]

So: the instructions there tell me that for multiple files, I should make a git repo to hold them.

Given how simple this case is to reproduce - the literal description describes the problem! - but how onerous it would be for me to make a whole GitHub repo (especially when in general, people should be migrating from GitHub for various reasons) just to host 3 very small files...

This is not a complex case - and you have spent more time trying to get me to follow onerous rules than it would take for you to make the reproducer following my instructions.

[mcanouil]

To be very clear, I cannot reproduce any issues using 1.8 and current development version.

Here are the steps with proper formatting:

1. Create a website project

quarto create project website i13977 i13977

2. add {{< include included.qmd >}} into index.qmd.

---
title: "i13977"
---

This is a Quarto website.

To learn more about Quarto websites visit <https://quarto.org/docs/websites>.

{{< include included.qmd >}}

3. included.qmd file being

::: {.callout-note}

{{< lipsum 1 >}}

::: {.callout-warning}

{{< lipsum 1 >}}

:::

:::

If you don't want to provide a clear depiction of the issue and properly format your posts by editing them using standard markdown syntax, I'm afraid there is nothing that can be done at this point.

---

A quick reminder about the Code of Conduct: https://github.com/quarto-dev/quarto-cli?tab=coc-ov-file