quarto publish Jupyter error

[michaelschulte]

On a Mac in RStudio

I am trying to run
quarto publish netlify

which ends with a long list of errors starting with:
Starting python3 kernel...Traceback (most recent call last): File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/runpy.py", line 197, in _run_module_as_main

after running
quarto check

(attached below)
I get:

(-) Checking Jupyter engine render....Traceback (most recent call last):
File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/runpy.py", line 197, in _run_module_as_main ...

So I re-install Jupyter (and then Jupyterlab) ...

there error messages remain the same.
I fear that there is some hiccup with homebrew and pip but I am not sure ...
Any help appreciated!

Michael

quarto_check_outpput.txt

[mcanouil]

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

You can share a Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).

````qmd
---
title: "Reproducible Quarto Document"
format: html
---

This is a reproducible Quarto document using `format: html`.
It is written in Markdown and contains embedded R code.
When you run the code, it will produce a plot.

```{r}
plot(cars)
```

The end.
````

[michaelschulte]

I could narrow it down on a Jupyter notebook (not very surprising)

I get this:

`Starting python3 kernel...Traceback (most recent call last):
File "/Applications/quarto/share/jupyter/jupyter.py", line 21, in
from notebook import notebook_execute, RestartKernel
File "/Applications/quarto/share/jupyter/notebook.py", line 17, in
import nbformat
ModuleNotFoundError: No module named 'nbformat'
Python 3 installation:
Version: 3.11.3
Path: /opt/homebrew/opt/[email protected]/bin/python3.11
Jupyter: (None)

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

ERROR: Error
at renderFiles (file:///Applications/quarto/bin/quarto.js:86653:30)
at async render (file:///Applications/quarto/bin/quarto.js:90675:21)
at async renderForPublish (file:///Applications/quarto/bin/quarto.js:121240:33)
at async renderForPublish (file:///Applications/quarto/bin/quarto.js:109082:24)
at async handlePublish (file:///Applications/quarto/bin/quarto.js:108988:26)
at async publishDocument (file:///Applications/quarto/bin/quarto.js:121342:38)
at async publish5 (file:///Applications/quarto/bin/quarto.js:121438:132)
at async doPublish (file:///Applications/quarto/bin/quarto.js:121394:13)
at async publishAction (file:///Applications/quarto/bin/quarto.js:121430:13)
at async Command.fn (file:///Applications/quarto/bin/quarto.js:121382:9)`

running this:

---
title: "TestPage"
echo: false
jupyter: python3
section-divs: false
keep-md: true
---

# Header

[michaelschulte]

small followup:

from the RStudio console I get this:

`Rendering for publish:

ERROR: Jupyter kernel 'python3.9' not found.

Error: Jupyter kernel 'python3.9' not found.
at jupyterKernelspecFromMarkdown (file:///Applications/quarto/bin/quarto.js:53189:35)
at async quartoMdToJupyter (file:///Applications/quarto/bin/quarto.js:53022:36)
at async createNotebookforTarget (file:///Applications/quarto/bin/quarto.js:55426:16)
at async Object.target (file:///Applications/quarto/bin/quarto.js:55219:18)
at async fileExecutionEngineAndTarget (file:///Applications/quarto/bin/quarto.js:58028:20)
at async renderContexts (file:///Applications/quarto/bin/quarto.js:82630:34)
at async Object.renderFormats (file:///Applications/quarto/bin/quarto.js:82683:26)
at async inputTargetIndex (file:///Applications/quarto/bin/quarto.js:83499:21)
at async resolveInputTarget (file:///Applications/quarto/bin/quarto.js:83578:19)
at async resolveItem (file:///Applications/quarto/bin/quarto.js:93620:26)`

I tried to switch python versions in Global Options and in Project Options ... without change

[mcanouil]

Please as I said, we need a "working" example.
Providing multiple "kernel not found" won't really help us help you.

Also, could you share the results of quarto check (not as a file) within a project where you have the errors?

Finally, could you user the GitHub toolbar to format your messages? For example, code in code blocks.
This would be very appreciated as it would improve the reading experience.
Thanks!

[michaelschulte]

Hi,

thanks for your reply - sorry for not following the conventions!

I ran:

---
title: "TestPage"
echo: false
jupyter: python3
section-divs: false
keep-md: true
---

# Header

quarto check gives me (would you want the output in a code block?):

[✓] 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: 1.3.340
      Path: /Applications/quarto/bin

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

[✓] Checking Python 3 installation....OK
      Version: 3.9.6
      Path: /Library/Developer/CommandLineTools/usr/bin/python3
      Jupyter: 5.0.0
      Kernels: python3

(/) Checking Jupyter engine render....Traceback (most recent call last):
  File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/Users/michael/Library/Python/3.9/lib/python/site-packages/ipykernel_launcher.py", line 15, in <module>
    from ipykernel import kernelapp as app
  File "/Users/michael/Library/Python/3.9/lib/python/site-packages/ipykernel/kernelapp.py", line 51, in <module>
    from .ipkernel import IPythonKernel
  File "/Users/michael/Library/Python/3.9/lib/python/site-packages/ipykernel/ipkernel.py", line 17, in <module>
    from .comm import CommManager
  File "/Users/michael/Library/Python/3.9/lib/python/site-packages/ipykernel/comm/__init__.py", line 1, in <module>
    from .comm import *  # noqa
  File "/Users/michael/Library/Python/3.9/lib/python/site-packages/ipykernel/comm/comm.py", line 12, in <module>
    from ipykernel.kernelbase import Kernel
  File "/Users/michael/Library/Python/3.9/lib/python/site-packages/ipykernel/kernelbase.py", line 35, in <module>
    import psutil
  File "/Users/michael/Library/Python/3.9/lib/python/site-packages/psutil/__init__.py", line 123, in <module>
    from . import _psosx as _psplatform
  File "/Users/michael/Library/Python/3.9/lib/python/site-packages/psutil/_psosx.py", line 13, in <module>
    from . import _psposix
  File "/Users/michael/Library/Python/3.9/lib/python/site-packages/psutil/_psposix.py", line 28, in <module>
    from . import _psutil_osx
ImportError: dlopen(/Users/michael/Library/Python/3.9/lib/python/site-packages/psutil/_psutil_osx.abi3.so, 0x0002): tried: '/Users/michael/Library/Python/3.9/lib/python/site-packages/psutil/_psutil_osx.abi3.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/michael/Library/Python/3.9/lib/python/site-packages/psutil/_psutil_osx.abi3.so' (no such file), '/Users/michael/Library/Python/3.9/lib/python/site-packages/psutil/_psutil_osx.abi3.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))
2023-05-13 09:22:53,942 - traitlets - ERROR - Error occurred while starting new kernel client for kernel 86430eba-9cd3-4b36-af40-873f50a00494: Kernel died before replying to kernel_info


Kernel died before replying to kernel_info
[✓] Checking Jupyter engine render....OK

Does this help?

[mcanouil]

The issue has nothing to do with Quarto, but with your Jupyter/Python setup.
It appears your installation of Python is faulty, as highlighted in the error from quarto check.

but is an incompatible architecture (have 'x86_64', need 'arm64')

You might want to fix your setup.
For help about this, I suggest to look on platforms more dedicated to Python, such as StackExchange or StackOverflow.

[stewartli]

I reinstalled jupyterlab. It works well. Thanks.