debugging advice for main.lua errors

[anielsen001]

Description

I'm getting an error when I try to render to a jupyter notebook, but i don't get the error if I just make a webpage. It looks like some kind of formatting issue in my qmd file. Is there a way to find out more details about where the error is? I see line numbers that refer to the main.lua script, but nothing referring to my inputs. Is there a way to find out where the error is so that I can try to address it?

The error looks like this:

[INFO] Running filter /opt/quarto/share/filters/main.lua
Error running filter /opt/quarto/share/filters/main.lua:
Block, list of Blocks, or compatible element expected, got table
	while retrieving function argument content
	while retrieving arguments for function Div
stack traceback:
	/opt/quarto/share/filters/main.lua:20822: in field 'render'
	/opt/quarto/share/filters/main.lua:835: in local 'filter_fn'
	/opt/quarto/share/filters/main.lua:302: in function </opt/quarto/share/filters/main.lua:292>
	(...tail calls...)
	[C]: in ?
	[C]: in method 'walk'
	/opt/quarto/share/filters/main.lua:224: in function </opt/quarto/share/filters/main.lua:214>
	(...tail calls...)
	/opt/quarto/share/filters/main.lua:936: in local 'callback'
	/opt/quarto/share/filters/main.lua:954: in upvalue 'run_emulated_filter_chain'
	/opt/quarto/share/filters/main.lua:990: in function </opt/quarto/share/filters/main.lua:987>
stack traceback:
	/opt/quarto/share/filters/main.lua:224: in function </opt/quarto/share/filters/main.lua:214>
	(...tail calls...)
	/opt/quarto/share/filters/main.lua:936: in local 'callback'
	/opt/quarto/share/filters/main.lua:954: in upvalue 'run_emulated_filter_chain'
	/opt/quarto/share/filters/main.lua:990: in function </opt/quarto/share/filters/main.lua:987>

[mcanouil]

Could you share a small self-contained "working" (reproducible) example to work with, i.e., a complete Quarto document or a Git repository? Thanks.

The usual debugging step is to make a reproducible example because it makes it easier to see what input is causing this (it could be a Quarto bug).

Note that sharing an error code without context is unlikely to get you with a concrete solution (here and anywhere else).

See https://quarto.org/docs/troubleshooting/index.html for the troubleshooting guide.

---

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

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

[anielsen001]

I will work to make one. The file I'm working with is quite large and complex. I was hoping to find a way to narrow down how to locate the problem within my file to create an example.

As a bit of context, I've been working on this as a html output for a while. The computations are complex and when I also output a ipynb format, quarto recomputes everything twice, so I disable the ipynb output until I'm done, then I reenable the ipynb output for the final product. because of this I don't know where to start looking for the issue. I can go thru and remove each section one at a time, but that will take a while.

I guess my question is if there is a way to find the location of the error in my code.

[mcanouil]

From the error message, I would assume it's related to a table in the wrong place which make me think are you using Quarto 1.3?

[anielsen001]

No, here's my quarto check output.

quarto check
Quarto 1.4.549
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.11: OK
      Dart Sass version 1.69.5: OK
      Deno version 1.37.2: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.4.549
      Path: /opt/quarto/bin

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

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

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

[✓] Checking Python 3 installation....OK
      Version: 3.11.8
      Path: /opt/project/venv_sp2024/bin/python3
      Jupyter: 5.7.2
      Kernels: python3

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

[✓] Checking R installation...........OK
      Version: 4.3.2
      Path: /usr/lib/R
      LibPaths:
        - /usr/local/lib/R/site-library
        - /usr/lib/R/site-library
        - /usr/lib/R/library
      knitr: 1.45
      rmarkdown: 2.25

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

[mcanouil]

So, Unlikely to be what I had in mind.

Small trick for you if you are using knitr.
Add a code cell with: knitr::knit_exit()
This will make the rendering happens until this command, so you could move this toward the end of your document (or backward).
Workflow:

1. put it in the middle
2. if it fails: move it to the middle of the first half of your document
   if it succeed: move it to the middle of the second half of your document
3. iterate using this approach to get down to the part leading to the issue (which I still think is a syntax issue with a table and/or a Quarto bug regarding that table)

[cderv]

To help debug, you could also activate Verbose mode and stack trace. It could say more that the current error
https://quarto.org/docs/troubleshooting/#verbose-mode

You could also try latest stable version 1.4, and possibly dev version of Quarto in case this is fixed already

[cscheid]

(And, just to be clear, this is a Quarto bug! no crashes like that should happen.)

[Steinthal]

I got a similar error yesterday after pasting in some text from Quicklook and could figure out what the cause was (in my case): The quotation marks in »widths="1.6"« (Quarto 1.5.55). Here's the the reproducible example:

---
title: "main.lua error"
format: pdf
---

# Test

::: {.list-table widths=“1,6“ header-rows=0}
* - n/a
  - Not applicable, not relevant

:::

[mcanouil]

You need straight double quotes.
Other symbols are not valid (that's not a Quarto specificity).

[Steinthal]

I know. That’s why I wrote the quotation mark was the cause of that error. It’s just meant as one example that produces the error or at least a similar error.

[mcanouil]

FYI, VSCode and other IDEs can detect these issues likely coming from copy/paste.

[Steinthal]

Thanks, that’s good to know. I’ll check Positron for that feature.

[mbellitti]

The following example throws an error on quarto 1.5.54

---
title: "Minimal example"
format: gfm
---

```{python}
#| label: fig-sin
import matplotlib.pyplot as plt
import numpy as np

x = np.linspace(0,1,10)
y = np.sin(x)

plt.plot(x,y)
```

The error is the following:

Error running filter /home/opt/quarto-1.5.54/share/filters/main.lua:
Block, list of Blocks, or compatible element expected, got table
        while retrieving function argument blocks
        while retrieving arguments for function Blocks
stack traceback:
        /home/opt/quarto-1.5.54/share/filters/main.lua:22460: in field 'render'
        /home/opt/quarto-1.5.54/share/filters/main.lua:1233: in local 'filter_fn'
        /home/opt/quarto-1.5.54/share/filters/main.lua:635: in function </home/opt/quarto-1.5.54/share/filters/main.lua:625>
        (...tail calls...)
        [C]: in ?
        [C]: in method 'walk'
        /home/opt/quarto-1.5.54/share/filters/main.lua:557: in function </home/opt/quarto-1.5.54/share/filters/main.lua:546>
        (...tail calls...)
        /home/opt/quarto-1.5.54/share/filters/main.lua:1334: in local 'callback'
        /home/opt/quarto-1.5.54/share/filters/main.lua:1352: in upvalue 'run_emulated_filter_chain'
        /home/opt/quarto-1.5.54/share/filters/main.lua:1388: in function </home/opt/quarto-1.5.54/share/filters/main.lua:1385>
stack traceback:
        /home/opt/quarto-1.5.54/share/filters/main.lua:557: in function </home/opt/quarto-1.5.54/share/filters/main.lua:546>
        (...tail calls...)
        /home/opt/quarto-1.5.54/share/filters/main.lua:1334: in local 'callback'
        /home/opt/quarto-1.5.54/share/filters/main.lua:1352: in upvalue 'run_emulated_filter_chain'
        /home/opt/quarto-1.5.54/share/filters/main.lua:1388: in function </home/opt/quarto-1.5.54/share/filters/main.lua:1385>

It sounds like it has something to do with the gfm output format, it works correctly if I render to html. The first time I encountered this bug I was rendering my project to both gfm and html, and changing that to just render html works as expected. I was using gfm because it gives a nice preview on GitHub.

[cderv]

Thanks for the report. I can reproduce and I opened an issue for this.

[cderv]

• Lua filter error with gfm for a crossref figure  #10358