Quarto in Rstudio says Julia is not found

[ghost]

Description

Hello,

I am trying the example from the doc, working on Ubuntu 22.04

---
title: "Plots Demo"
author: "Norah Jones"
date: "5/22/2021"
format:
  html:
    code-fold: true
jupyter: julia-1.9.3
---

## Parametric Plots

Plot function pair (x(u), y(u)). 
See @fig-parametric for an example.

```{julia}
#| label: fig-parametric
#| fig-cap: "Parametric Plots"

using Plots

plot(sin, 
     x->sin(2x), 
     0, 
     2π, 
     leg=false, 
     fill=(0,:lavender))
```

The output is

Warning in system2("bash", "-l -c 'which julia'", stdout = TRUE) :
  running command ''bash' -l -c 'which julia'' had status 1
sh: 1: NA: not found
Error in julia_setup() : Julia is not found.
Error in julia_setup() : Julia is not found.

But Julia is installed in my system. If I open a terminal and type julia I end up in the REPL.
How do I initialize julia_setup()?

Thank you

[cderv]

I am surprised by the content of your document compared to the error message you get.

I believe the error is from JuliaCall R package, but your .qmd file contains jupyter: julia-1.9.3 in YAML so should use Python and Jupyter to run Julia with IJulia.

Can you share you quarto version ?
Can you try quarto render in Terminal ?

Can you restart and be sure that your environment is clean before rendering the file ?

[ghost]

I rebooted the computer.

quarto --version
1.3.450

and the render

quarto render MA_mutation_analysis.qmd 
ERROR: Jupyter kernel 'julia-1.9.3' not found.

Error: Jupyter kernel 'julia-1.9.3' not found.
    at jupyterKernelspecFromMarkdown (file:///opt/quarto/bin/quarto.js:53188:35)
    at async quartoMdToJupyter (file:///opt/quarto/bin/quarto.js:53021:36)
    at async createNotebookforTarget (file:///opt/quarto/bin/quarto.js:55428:16)
    at async Object.target (file:///opt/quarto/bin/quarto.js:55221:18)
    at async fileExecutionEngineAndTarget (file:///opt/quarto/bin/quarto.js:58033:20)
    at async renderFiles (file:///opt/quarto/bin/quarto.js:86522:46)
    at async render (file:///opt/quarto/bin/quarto.js:90681:21)
    at async Command.fn (file:///opt/quarto/bin/quarto.js:90856:32)
    at async Command.execute (file:///opt/quarto/bin/quarto.js:8437:13)
    at async quarto (file:///opt/quarto/bin/quarto.js:127545:5)

I really don't get why it doesn't find julia

[cderv]

Yes error is now clearer and correctly tied to Jupyter. Follow installation as mentioned above and check that you are using a correct engine that you have setup.

[ghost]

Thing is, I scrupulously followed the instructions above. I am gonna start all over again. If it still doesn't work I will use Pluto for Julia. Not related but, I did my studies with Rstudio 10 years ago and it's fantastic all the development that have been made.

Cheers

EDIT: doesn't work, I also tried the route of an independent Jupyter install... I will use Pluto as said since I don't have too much time to spend finding a solution to this. That being said if this is of interest to you, you can still ask details about my install, I am ok with providing details.

Thanks.

[ghost]

Since I am more stubborn ....

quarto check jupyter

[✓] Checking Python 3 installation....OK
      Version: 3.10.12
      Path: /usr/bin/python3
      Jupyter: 5.3.1
      Kernels: julia-1.9, python3

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

How can quarto finds jupyter in command line in a bash shell, but not in Rstudio?

[cderv]

Kernels: julia-1.9, python3

This shows you that kernel name is julia-1.9 and not julia-1.9.3 as you put in your YAML header in .qmd document. You should try with correct name in

jupyter: julia-1.9

[ghost]

Kernels: julia-1.9, python3

This shows you that kernel name is julia-1.9 and not julia-1.9.3 as you put in your YAML header in .qmd document

Indeed, just figured it out as you typed. Strange because it's Julia 9.3 that is installed. thanks for the support.