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Quarto Notebook not rendering #222

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farmacyst99 opened this issue Dec 10, 2024 · 10 comments
Closed

Quarto Notebook not rendering #222

farmacyst99 opened this issue Dec 10, 2024 · 10 comments

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@farmacyst99
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Hi, I'm using Pumas and need to use Quarto to prepare a document. But after giving the render command, the process gets stuck with no error or output. I'm trying to use the Julia engine. This is the output to quarto check

quarto check
Quarto 1.6.39
[✓] Checking environment information...
      Quarto cache location: /Users/farmacyst/Library/Caches/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: 1.6.39
      Path: /Applications/quarto/bin

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

[✓] Checking LaTeX....................OK
      Tex:  (not detected)

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

[✓] Checking Python 3 installation....OK
      Version: 3.9.6
      Path: /Library/Developer/CommandLineTools/usr/bin/python3
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

[✓] Checking R installation...........OK
      Version: 4.4.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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")

this is the front matter on the document:

---
title: "Untitled"
format: html
engine: julia
---

But as soon as I put quarto render filename I get no output or error.

I have tried running quarto render filename --execute-debug and get the following output:

quarto render brooks-model.qmd --execute-debug
- Transport file /Users/farmacyst/Library/Caches/quarto/julia/julia_transport.txt exists, reusing server.
- Transport file read successfully.
- Connecting to server at port 8000, pid 1577
- write command "isready" to socket server
- received server response
- Transport file read successfully.
- write command "run" to socket server

@MichaelHatherly
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But as soon as I put quarto render filename I get no output or error.

Does it hang and never complete, or does it complete but just display nothing?

@farmacyst99
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farmacyst99 commented Dec 10, 2024 via email

@MichaelHatherly
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Yes, it hangs and never completes.

Is this dependent on whether you have {julia} cells in the document? Or does it also hang even when there are no cells in the document?

@MichaelHatherly
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Can you try running the following command in the same terminal and then rerunning quarto render?

kill $(ps aux | grep '[j]ulia.*quartonotebookrunner\.jl' | awk '{print $2}')

@farmacyst99
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farmacyst99 commented Dec 10, 2024 via email

@MichaelHatherly
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ERROR: NotFound: Failed to spawn 'julia': No such file or directory (os
error 2)

That is the important part, it appears there is no julia binary found. Does julia run in that same terminal start up Julia, or does that fail as well?

@farmacyst99
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farmacyst99 commented Dec 10, 2024 via email

@MichaelHatherly
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No it does not start up in the same terminal, but I have the Julia app
installed via their website

If it does not start up then there is a more fundamental issue beyond QuartoNotebookRunner.jl that needs to be resolved that is more related to PumasDesktop setup. Please continue the discussion over in https://discourse.pumas.ai/t/quarto-notebook-not-rendering/1092/11 where this begun.

@farmacyst99
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farmacyst99 commented Dec 10, 2024 via email

@MichaelHatherly
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Closing as this is Pumas-specific. Continuation of the discussion is in the discourse thread.

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