.qmd converting to .R style on save...

[cjsrussell]

Hi All,

I have a .qmd file and use code chunks extensively. I have noticed that sometimes when I save the file all the code chunks are essentially removed, and comment lines added for spacing, see below.

This was originally a code chunk and now just appears to be a standard R script? Same thing has happened to the entire document a few times.

Any help is appreciated!

Thanks.

Original: (shown as image because chunk formatting breaks this post)

After save:

#
#
#
#
#
#
#
# columns

telcols <- colnames(survey_coded %>%
  dplyr::select(dplyr::starts_with("tel_")))

# code

# normal

survey_coded <- funCode(
  survey_coded,
  telcols,
  "agreement",
  FALSE
)

#
#
#
#
#
#
#

[sharon-wang]

Hi @cjsrussell! Could you please share a bit more info about your setup?

• Positron Version: Copy from the Positron > About Positron menu
• Any chance you can share the whole .qmd file or screen record the issue?
• Do you have any formatter extensions installed?
• Can you share your settings.json file? Run the command Preferences: Open User Settings (JSON) in the Command Palette

A tip! To include tex enclosed in triple backticks "```", you can use quadruple backticks "````":

````
```{r}
#code block
```
````

Here's a test .qmd file I am using -- so far I haven't been able to reproduce the issue in Positron 2025.04.0 build 204 on Mac.

---
title: "Untitled"
format: html
---

here is my quarto doc

```{r}
# columns

telcols <- colnames(survey_coded %>%
  dplyr::select(dplyr::starts_with("tel_")))

# code

# normal

survey_coded <- funCode(
  survey_coded,
  telcols,
  "agreement",
  FALSE
)
```

# another code chunk

```{r}
# iris
iris

# another comment

# hello

x <- mtcars

# bye

abc <- print('hi')

```

[cjsrussell]

Hi @sharon-wang,

Thanks for your response.

I'm using v2025.03.0, build 116, on Windows11.

It is happening across different .qmd files so I don't think it is file specific, and I also can't reliably recreate the issue myself. It happens only sometimes on save. Particularly odd is that It can happen when I save, but if I then undo it fixes it, and can usually save again and it doesn't happen...

I don't think I have any relevant extensions installed. Its a pretty minimal new install:

Those are all my extensions.

I also haven't done much with the settings in this regard, only turned on formatOnSave, which I will probably disable for now.

{
    "editor.inlineSuggest.syntaxHighlightingEnabled": true,
    "workbench.sideBar.location": "right",
    "workbench.colorTheme": "Default Positron Dark",
    "editor.fontFamily": "Fira Code",
    "editor.fontLigatures": true,
    "editor.fontVariations": false,
    "editor.fontWeight": "500",
    "problems.showCurrentInStatus": true,
    "files.autoSave": "afterDelay",
    "rstudio.keymap.enable": true,
    "editor.formatOnSave": true
}

editor and notebook default formatter is set to none.

Thanks, and thanks for the backticks tip!

[sharon-wang]

Thank you for the additional detail! I dug around and found #6867 which sounds like the same issue you're describing. From that discussion, it seems we think the issue may be in Quarto rather than Positron.

This issue was opened and should be the best place to follow further discussion: quarto-dev/quarto#683

[cjsrussell]

Thanks, @sharon-wang!