Quarto shows "KERNEL EXCEPTION" with Julia

[juliohm]

Bug description

I have an open book built with Quarto + Julia, and started noticing this error message in latest builds:

You can find the full log in the github repo: https://github.com/JuliaEarth/geospatial-data-science-with-julia/actions/runs/13157347110/job/36717424828

I also noticed that building chapters locally with quarto preview chapter.qmd is no longer functioning as before in the sense that the mouse cursor changes to a + symbol, and waits for me to click a few times, as if it is expecting input from the user.

These two bugs may be related to some recent update in the Julia kernel specifically. I don't know. How can I help debug it further?

Steps to reproduce

You can build the open book locally: https://github.com/JuliaEarth/geospatial-data-science-with-julia

Expected behavior

• No "KERNEL EXCEPTION" error message after each chapter is built
• No need to click with the mouse to proceed with build in quarto preview chapter.qmd

Actual behavior

• "KERNEL EXCEPTION" is shown after each chapter is built
• I need to click with the mouse a few times to see the result of quarto preview chapter.qmd

Your environment

Version: 1.92.2
Commit: fee1edb8d6d72a0ddff41e5f71a671c23ed924b9
Date: 2024-08-14T17:29:30.058Z
Electron: 30.1.2
ElectronBuildId: 9870757
Chromium: 124.0.6367.243
Node.js: 20.14.0
V8: 12.4.254.20-electron.0
OS: Linux x64 5.15.177-1-MANJARO

Julia Version 1.11.3
Commit d63adeda50d (2025-01-21 19:42 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 8 × Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, skylake)
Threads: 8 default, 0 interactive, 4 GC (on 8 virtual cores)
Environment:
  JULIA_NUM_THREADS = 8

Quarto check output

[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.1: OK
      Dart Sass version 1.55.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.3.450
      Path: /opt/quarto/bin

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

[✓] Checking Python 3 installation....OK
      Version: 3.13.1
      Path: /usr/bin/python3
      Jupyter: 5.7.2
      Kernels: python3, julia-1.11, julia-1.10, julia-1.9

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

[✓] Checking R installation...........OK
      Version: 4.4.2
      Path: /usr/lib64/R
      LibPaths:
        - /usr/lib/R/library
      knitr: (None)
      rmarkdown: (None)

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

[mcanouil]

You are running Quarto 1.3.450 which is 1 year and half old.
Please upgrade your version and report back.
https://quarto.org/docs/get-started/

[juliohm]

I don't see where we are fixing an old version. Our GitHub Actions use the official quarto-actions@v2:

https://github.com/JuliaEarth/geospatial-data-science-with-julia/blob/main/.github/workflows/publish.yml

Should this be fixed in the quarto-actions repository?

I will try to update Quarto locally anyways to see if the error persists.

[mcanouil]

The Quarto check is not from your CI?
Did you try debugging your workflow locally?

I'm afraid you'll have to debug locally first and come down to a smaller example targeting the code in your project causing this. Here some part of your code is causing the Jupyter kernel running IJulia to crash. Note that these components are not developed or maintained by the Quarto team. You actually might have the exact same issue without using Quarto at all (like using a Jupyter Notebook).
The Quarto team doesn't have the time to debug your whole project unfortunately.

Note also that Quarto since quite some time now has a native engine for Julia engine: julia, see https://quarto.org/docs/computations/julia.html#using-the-julia-engine.

[juliohm]

Will try to take a look at it today. First, I will try to update Quarto locally and maintain the same configuration I am using currently with jupyter: julia-1.11 in my _quarto.yml. Second, I will try to update to the latest Julia kernel with the engine: julia in all *.qmd files instead of the jupyter: julia-1.11 in _quarto.yml.

[juliohm]

I confirm that the "KERNEL EXCEPTION" message still shows up locally after updating Quarto. I forgot to mention that in both versions of Quarto I started to see local files created during the build: getopt, os, sys and sysconfig.

If I change from jupyter: julia-1.11 to the new engine: julia, the error message is gone.

Should this issue be closed and the jupyter engine deprecated?

For future reference, all one needs to do to use the newest engine is to add

---
engine: julia
---

at the top of every .qmd page with Julia code.

[cderv]

Should this issue be closed and the jupyter engine deprecated?

Jupyter engine is not deprecated but using IJulia through Jupyter is no more necessary now that native engine: julia is available.

So KERNEL_EXCEPTION issue here is related to IJulia kernel it seems. It will be hard to look at and identify even if quarto is at play in the issue.

I suggest we close this specific issue and watchout for possible more KERNEL_EXCEPTION in the future.

Thanks !