Issues with Running Code Chunks in Quarto on Positron

[erikdeluca]

Description

Hello everyone,

I am experiencing issues when using Quarto within Positron, specifically when attempting to include R or Python code chunks in my .qmd documents. While using the quarto preview command, different errors arise based on the language used in the chunk.

Here’s an example of my .qmd files:

file for R code:

---
title: "Test"
format: html
---

## R Code

```{r}
print("Hello, R!")
```

file for Python code:

---
title: "Test"
format: html
---

## Python Code

```{python}
print("Hello, Python!")
```

Errors Received:

• R: Encounter an error stating:

  Error in dir.exists(x) : file name conversion problem – name too long?
  Calls: … lapply -> FUN -> dir_exists -> -> dir.exists
  Execution halted
  

• Python: Encounter this error:

  PS D:\GitHub\testing> quarto preview d:/GitHub/testing/test.qmd --no-browser --no-watch-inputs
  ERROR: Impossible to access to the file. (os error 1920): stat 'C:\Users\erik4\AppData\Local\Microsoft\WindowsApps\python3.12.exe'
  
  Stack trace:
      at Object.statSync (ext:deno_fs/30_fs.js:425:3)
      at existsSync (file:///C:/Users/erik4/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:223:27)
      at getQuartoJupyterCapabilities (file:///C:/Users/erik4/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:30667:13)
      at jupyterCapabilities (file:///C:/Users/erik4/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:30582:34)
      at pythonExec (file:///C:/Users/erik4/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:30764:24)
      at Object.execute (file:///C:/Users/erik4/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:40546:35)
      at async renderExecute (file:///C:/Users/erik4/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:78033:27)
      at async renderFileInternal (file:///C:/Users/erik4/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:78201:43)
      at async renderFiles (file:///C:/Users/erik4/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:78069:17)
      at async render (file:///C:/Users/erik4/AppData/Local/Programs/Positron/resources/app/quarto/bin/quarto.js:82929:21)
  PS D:\GitHub\testing> 
  

Stack trace details have been provided in my Stack Overflow post.

What I've Tried:

1. Verified that both Python and R are correctly installed and in the system PATH.
2. Checked the project's folder permissions.
3. Tried reducing the project path length; the issue persists.
4. Updated Positron, Quarto, Python, and R to the latest versions.

Additional Information from Comments from Stack Overflow:

• The really strange thing is that the error only occurs with the shell created using the Preview button, and only for R, if I use a shell in Positron

I'd appreciate any help or suggestions. Thank you in advance!

R version: 4.4.2
Python version: 3.12.9

Quarto info:
From the Quarto Preview's shell I tried to run quarto check and this is the result:

  PS D:\GitHub\second-test> quarto check
  Quarto 1.6.42
  [>] Checking environment information...
        Quarto cache location: C:\Users\erik4\AppData\Local\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: 1.6.42
        Path: C:\Users\erik4\AppData\Local\Programs\Quarto\bin
        CodePage: 1252
  
  [>] Checking tools....................OK
        TinyTeX: v2025.01
        Chromium: (not installed)
  
  [>] Checking LaTeX....................OK
        Using: TinyTex
        Path: C:\Users\erik4\AppData\Roaming\TinyTeX\bin\windows\
        Version: 2024
  
  [>] Checking basic markdown render....OK
  
  ERROR: Impossibile accedere al file. (os error 1920): stat 'C:\Users\erik4\AppData\Local\Microsoft\WindowsApps\python3.12.exe'
  
  Stack trace:
      at Object.statSync (ext:deno_fs/30_fs.js:425:3)
      at existsSync (file:///C:/Users/erik4/AppData/Local/Programs/Quarto/bin/quarto.js:1988:27)    
      at getQuartoJupyterCapabilities (file:///C:/Users/erik4/AppData/Local/Programs/Quarto/bin/quarto.js:30756:13)
      at jupyterCapabilities (file:///C:/Users/erik4/AppData/Local/Programs/Quarto/bin/quarto.js:30671:34)
      at file:///C:/Users/erik4/AppData/Local/Programs/Quarto/bin/quarto.js:108525:22
      at withSpinner (file:///C:/Users/erik4/AppData/Local/Programs/Quarto/bin/quarto.js:83766:22)  
      at checkJupyterInstallation (file:///C:/Users/erik4/AppData/Local/Programs/Quarto/bin/quarto.js:108521:11)
      at check (file:///C:/Users/erik4/AppData/Local/Programs/Quarto/bin/quarto.js:108344:19)       
      at eventLoopTick (ext:core/01_core.js:175:7)
      at async Command.actionHandler (file:///C:/Users/erik4/AppData/Local/Programs/Quarto/bin/quarto.js:108666:5)

Then, in a new shell, I run again quarto check. While before the issue was with Python, now it's with R.

  PS D:\GitHub\second-test> quarto check
  Quarto 1.6.42
  [>] Checking environment information...
        Quarto cache location: C:\Users\erik4\AppData\Local\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
        Path: C:\Users\erik4\AppData\Local\Programs\Quarto\bin    
        CodePage: 1252
  
  [>] Checking tools....................OK
        TinyTeX: v2025.01
        Chromium: (not installed)
  
  [>] Checking LaTeX....................OK
        Using: TinyTex
        Path: C:\Users\erik4\AppData\Roaming\TinyTeX\bin\windows\ 
        Version: 2024
  
  [>] Checking basic markdown render....OK
  
  [>] Checking Python 3 installation....OK
        Version: 3.12.1
        Path: C:/Users/erik4/AppData/Local/Programs/Python/Python312/python.exe
        Jupyter: 5.7.2
        Kernels: python3
  
  [>] Checking Jupyter engine render....OK
  
  [>] Checking R installation...........OK
        Version: 4.4.2
        Path: C:/PROGRA~1/R/R-44~1.2
        LibPaths:
          - C:/Users/erik4/AppData/Local/R/win-library/4.4        
          - C:/Program Files/R/R-4.4.2/library
        knitr: 1.49
        rmarkdown: 2.29
  
  (-) Checking Knitr engine render......ERROR: Error in dir.exists(x) : file name conversion problem -- name too long?
  Calls: <Anonymous> ... lapply -> FUN -> dir_exists -> <Anonymous> -> dir.exists
  Execution halted
  
  [>] Checking Knitr engine render......OK

[mcanouil]

Could you kindly provide a more realistic example along with the full stack trace?
It seems you are suggesting two different errors, yet both languages are placed within the same document. Does this mean you're using a combination of knitr and reticulate?
Additionally, could you please clarify the steps required to reproduce the issue? (If possible, including a screencast might be helpful.)
You mentioned, "Updated Positron, Quarto, Python, and R to the latest versions."
However, the latest version of R is 4.4.3, and for Python, it’s 3.13.2.

What is the output of quarto check?

[erikdeluca]

Thank you so much for your help. I really appreciate it

[cderv]

I cannot render the document using Positron, although it works with RStudio.

Do you mean quarto render works in RStudio IDE ?

Does quarto render work in your Windows Terminal ?

I mean is the problem only in POSITRON ? Positron does handle R directly for their console integration feature, so maybe there is a conflict somewhere.

[erikdeluca]

I've just tried and quarto check (and the other commands) works only in RStudio's shell.

The problem is specific within knitr. So, if I render a document, without R code, everything works.

[mcanouil]

Would you mind sharing a screencast of what works and where?

[cderv]

I've just tried and quarto check (and the other commands) works only in RStudio's shell.

If this works in RStudio shell (I guess your referring to Terminal no R console), then it means quarto CLI itself if correctly finding R and using it. You can try quarto render inside RStudio IDE, or cliking the render button to confirm.

It would be good to try in an external Terminal. Powershell for example - without any IDE.

If the problem is only in Positron, then something is happening in the Positron context regarding your environment and how Quarto detects R binary.

[Cidre-Gesplan]

Hello. I opened also a discusion regarding this issue posit-dev/positron#6693
I don't have any problem running Quarto files with Python code, only with R.

What works for me is to use the R package within Positron, so it can be a workaround while this issue persists.

quarto::quarto_preview()