Error resolving header-includes with juliaengine

[MHellmund]

Bug description

Quarto version: pull from today
_quarto.yml:

project:
    type: book

book:
    chapters:
        - index.qmd

index.qmd:

---
engine: julia
---

```{julia}
?for
```

quarto render --to html ends with

FATAL (/home/hellmund/quarto-cli/src/resources/filters/./quarto-init/includes.lua:54) An error occurred:
Error resolving header-includes- unable to open file <script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" integrity="sha512-c3Nl8+7g4LMSTdrm621y7kf9v3SDPnhxLNhcjFJbKECVnmZHTdo+IRO05sNLTH/D3vA6u1X32ehoLC7WFVdheg==" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.5.1/jquery.min.js" integrity="sha512-bLT0Qm9VnAYZDflyKcBaQ2gg0hSYNQrJ8RilYldYQ1FxQYoCLtUjuuRuZo+fjqhx/qtq/1itJ0C2ejDxltZVFg==" crossorigin="anonymous" data-relocate-top="true"></script>
<script type="application/javascript">define('jquery', [],function() {return window.jQuery;})</script>

further observations:

• This bug does not occur in quarto 1.7.13.
• This bug does not occur without project file _quarto.yml.
• The julia code produces, among others, an output cell of type text/html. This triggers jsWidgets=true in widgets.ts, which is not necessary here but not a problem.
• My guess is that includes.lua is somehow called twice and the second run produces the error.

Steps to reproduce

No response

Actual behavior

No response

Expected behavior

No response

Your environment

OS: archlinux

Quarto check output

Quarto 99.9.9
[✓] Checking environment information...
      Quarto cache location: /home/hellmund/.cache/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.4.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.46.3: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
      commit: 7bacf5f2abd9fa2792c5e9d89a3c200be8916390
      Path: /home/hellmund/quarto-cli/package/dist/bin

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

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

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

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

[✓] Checking Python 3 installation....OK
      Version: 3.13.1
      Path: /usr/bin/python3
      Jupyter: 5.7.2
      Kernels: julia-1.11-t, julia-1.11, haskell, python3

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

[✓] Checking R installation...........OK
      Version: 4.4.2
      Path: /usr/lib64/R
      LibPaths:
        - /home/hellmund/R/x86_64-pc-linux-gnu-library/4.4
        - /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")

[cderv]

Thanks for the reproducible example. I can reproduce. So I looked into it.

For the context, we do set jswidget to true because the cell output has display_data of type text/html

quarto-cli/src/core/jupyter/widgets.ts

Lines 28 to 36 in d07b3eb

	// a 'javascript' widget doesn't use the jupyter widgets protocol, but rather just injects
	// text/html or application/javascript directly. futhermore these 'widgets' often assume
	// that require.js and jquery are available. for example, see:
	// - https://github.com/mwouts/itables
	// - https://plotly.com/python/
	const jsWidgets = haveOutputType(
	nb,
	[kApplicationJavascript, kTextHtml],
	);

This is why the require.js dep is added in head

quarto-cli/src/core/jupyter/widgets.ts

Lines 100 to 112 in d07b3eb

	// write required dependencies into head
	const head: string[] = [];
	if (haveJavascriptWidgets || haveJupyterWidgets) {
	head.push(
	'<script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" integrity="sha512-c3Nl8+7g4LMSTdrm621y7kf9v3SDPnhxLNhcjFJbKECVnmZHTdo+IRO05sNLTH/D3vA6u1X32ehoLC7WFVdheg==" crossorigin="anonymous"></script>',
	);
	head.push(
	'<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.5.1/jquery.min.js" integrity="sha512-bLT0Qm9VnAYZDflyKcBaQ2gg0hSYNQrJ8RilYldYQ1FxQYoCLtUjuuRuZo+fjqhx/qtq/1itJ0C2ejDxltZVFg==" crossorigin="anonymous" data-relocate-top="true"></script>',
	);
	head.push(
	"<script type=\"application/javascript\">define('jquery', [],function() {return window.jQuery;})</script>",
	);
	}

The addition is correctly done using a file which is expected for include-in-header

However, somehow the file path is replaced in place by file content. And this is creating the problem as include-in-header is supposed to be file.

The rest was more challenging to understand and debug.

This bug does not occur without project file _quarto.yml.

This was the puzzling part, but I ended up finding this is was related to freeze process, which is only for project.

After execution, quarto compute freeze file

quarto-cli/src/command/render/render-files.ts

Lines 235 to 242 in d07b3eb

	// write the freeze file if we are in a project
	if (context.project && !context.project.isSingleFile && canFreeze) {
	// write the freezer file
	const freezeFile = freezeExecuteResult(
	context.target.source,
	output,
	executeResult,
	);

and this process does resolve includes

quarto-cli/src/command/render/freeze.ts

Lines 50 to 74 in d07b3eb

	export function freezeExecuteResult(
	input: string,
	output: string,
	result: ExecuteResult,
	) {
	// resolve includes within executeResult
	const innerResult = {
	...result,
	} as ExecuteResult;
	const resolveIncludes = (
	name: "include-in-header" | "include-before-body" | "include-after-body",
	) => {
	if (innerResult.includes) {
	if (innerResult.includes[name]) {
	innerResult.includes[name] = innerResult.includes[name]!.map((file) =>
	// Storing file content using LF line ending
	format(Deno.readTextFileSync(file), LF)
	);
	}
	}
	};
	resolveIncludes(kIncludeInHeader);
	resolveIncludes(kIncludeBeforeBody);
	resolveIncludes(kIncludeAfterBody);

and now it does it without protecting modification in place. This is a side effect of

• perf - remove cloneDeep calls #11993

We need to make sure here to not modify by refernce as this will create this problem.

Thanks a lot for the report! We'll fix it.

[cscheid]

Thanks for catching this, @cderv!

[cderv]

Thanks for the report @MHellmund !

[TomBener]

I also encountered a similar issue in version 1.7.14:

FATAL (/Applications/quarto/share/filters/main.lua:3975) An error occurred:
Error resolving header-includes- unable to open file <link href="index_files/libs/tabwid-1.1.3/tabwid.css" rel="stylesheet" />
<script src="index_files/libs/tabwid-1.1.3/tabwid.js"></script>

[mcanouil]

@TomBener thanks for your interest. Note that a simple thumb up reaction on the original post is enough and avoid triggering notifications to all participants, unless you want to share additional information.
The fix is not released but is on main as you can see in the history logs.

[cderv]

I am building right now 1.7.15, so when it is done, the fix will be available in pre-release