R code formatting

[strengejacke]

I'm not sure if I'm missing something, but is it possible to format R code? I have enabled settings:

  "editor.defaultFormatter": "positron.positron-r",
  "editor.formatOnType": true,

And there are some defined keybindings:

But it doesn't seem to work.

Setup

Positron Version: 2024.12.0 (system setup) build 80
Code - OSS Version: 1.93.0
Commit: c3c4896
Date: 2024-11-26T02:46:23.686Z
Electron: 30.4.0
Chromium: 124.0.6367.243
Node.js: 20.15.1
V8: 12.4.254.20-electron.0
OS: Windows_NT x64 10.0.26100

R 4.4.2

E.g. this code can't be formatted.

data(mtcars)
if(mtcars$mpg>5) {
  print("hi")
}

Result in VSCode and RStudio:

data(mtcars)
if (mtcars$mpg > 5) {
  print("hi")
}

[lionel-]

Do you have styler installed? We currently depend on it (#2251).

[strengejacke]

Yes:

packageVersion("styler")
#> [1] ‘1.10.3’

[strengejacke]

This also happens when I press Shift+Alt+F:

[zwallen]

I am also running into this problem. I have the same version of styler installed as well.

Additionally, when I have my cursor within an R chunk and try to format it via Ctrl + K and then Ctrl + F I get an error message which seems to stem from Quarto (I have it as the default formatter for notebooks).

The .vdoc.r intermediate file is produced but it only shows the code of the chunk as is and additionally shows flags over certain functions like the following

[juliasilge]

I noticed that this report plus #5531 were both on Windows, so I just tried formatting ("Format Document" and "Format Selection") with:

Positron Version: 2024.12.0 (system setup) build 80
Code - OSS Version: 1.93.0
Commit: c3c4896
Date: 2024-11-26T02:46:23.686Z
Electron: 30.4.0
Chromium: 124.0.6367.243
Node.js: 20.15.1
V8: 12.4.254.20-electron.0
OS: Windows_NT x64 10.0.19045

This did work for me correctly. So no clue yet!

Question 1

Can you make sure your R kernel log level is debug?

And then can try to format and visit the Output channel for "R 4.4.0: Kernel" (or your equivalent) to confirm you don't see any messages like:

[R] 2024-11-27T21:34:11.410104Z INFO Received shell notification: JupyterMessage { zmq_identities: [[112, 111, 115, 105, 116, 114, 111, 110, 45, 115, 104, 101, 108, 108]], header: JupyterHeader { msg_id: "f3039d98-a7db-45ec-aa7a-6b845618e4fb", session: "7348364a16fb77d781f954f7237f3b19", username: "juliasilge", date: "2024-11-27T21:34:11.409Z", msg_type: "comm_msg", version: "5.0" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-1-408692b6", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("packageVersion"), "params": Array [String("styler"), Null]}} } }
[R] at crates/amalthea/src/socket/shell.rs:232
[R]
[R] 2024-11-27T21:34:11.412644Z INFO Received shell request: JupyterMessage { zmq_identities: [[112, 111, 115, 105, 116, 114, 111, 110, 45, 115, 104, 101, 108, 108]], header: JupyterHeader { msg_id: "7a2926b4-62d9-42b2-a70f-a84369293e64", session: "7348364a16fb77d781f954f7237f3b19", username: "juliasilge", date: "2024-11-27T21:34:11.412Z", msg_type: "execute_request", version: "5.0" }, parent_header: None, content: ExecuteRequest { code: "styler::style_file('/var/folders/hv/hzsmmyk9393_m7q3nscx1slc0000gn/T/styler-b003adf1-82bb-4929-938e-5ef446e45cea.R')", silent: true, store_history: false, user_expressions: Object {}, allow_stdin: false, stop_on_error: false } }
[R] at crates/amalthea/src/socket/shell.rs:185

Question 2

Can you confirm it is only the formatter that isn't working? We set that up here, so I'd be interested in knowing if both commands and tasks are provided correctly. Can you confirm that you can successfully use:

• The command "R: New R File"
• Something that is a task, such as "R: Render document with R Markdown"

Question 3

We have a new kernel supervisor in the latest release. Can you turn it off, restart Positron, and check if you still see the problem?

[lijiaqi-github]

I am reporting some of my confirmations here. Sorry I don't quite understand some of the instructions you gave, so I can only confirm the parts I understand.

Question 1

My previous R kernel log level is warn (default), I change it to info.

I downloaded the R 4.4.0, but I donot know how to visit the Output channel for "R 4.4.0: Kernel" (or your equivalent) . so I cannot confirm this instruction.

Question 2

I do not have enough knowledge to understand those code you give in that new link. so I cannot comfirm this instruction.

But ctrl + shift + n for creating New R File is working for me. Also, ctrl + shift + c and alt + - are working for me. Those are shortcuts I often used, so I can confirm that they work well.

Question 3

I turned off kernel supervisor and restarted Positron.

This is my settings.json:, you can find that I changed R kernel log level and turned off kernel supervisor.

{
"workbench.colorTheme": "Default Positron Dark",
"quarto.visualEditor.spelling": true,
"js/ts.implicitProjectConfig.checkJs": true,
"python.analysis.diagnosticMode": "workspace",
"git.confirmSync": false,
"explorer.confirmDelete": false,
"problems.defaultViewMode": "table",
"problems.showCurrentInStatus": true,
"workbench.editorAssociations": {
"*.tiff": "default"
},
"editor.renderWhitespace": "all",
"editor.autoClosingBrackets": "beforeWhitespace",
"editor.autoClosingDelete": "never",
"positron.r.pipe": "%>%",
"editor.rulers": [
80,
100
],
"editor.minimap.enabled": true,
"editor.minimap.maxColumn": 200,
"application.experimental.positronPlotsInEditorTab": true,
"rstudio.keymap.enable": true,

"positron.r.kernel.logLevel": "info",
"positronKernelSupervisor.enable": false

}

Unfortunately, after doing all this, ctrl + shift + a is still not working. Hopefully someone else can bring good news.

[zwallen]

Ok so tried my hand at your questions...

Question 1

I set the Positron > R > Kernel: Log Level to debug as suggested and got the following debug output when I performed formatting of a chunk of R code (Ctrl + K Ctrl + F):

[R]   2024-11-29T00:59:59.319401Z  INFO  Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 53, 102, 57, 56, 100, 57, 98, 54], [114, 45, 53, 102, 57, 56, 100, 57, 98, 54]], header: JupyterHeader { msg_id: "5be715c9", session: "r-5f98d9b6", username: "zdw12", date: "2024-11-29T00:59:59.318Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-1-eebad9ab", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("packageVersion"), "params": Array [String("styler"), Null]}} } }
[R]     at crates\amalthea\src\socket\shell.rs:232
[R] 
[R]   2024-11-29T00:59:59.331930Z  INFO  Received shell request: JupyterMessage { zmq_identities: [[114, 45, 53, 102, 57, 56, 100, 57, 98, 54], [114, 45, 53, 102, 57, 56, 100, 57, 98, 54]], header: JupyterHeader { msg_id: "e4b3e58a-9ecf-4c08-aa2f-b9771c34ef73", session: "r-5f98d9b6", username: "zdw12", date: "2024-11-29T00:59:59.331Z", msg_type: "execute_request", version: "5.3" }, parent_header: None, content: ExecuteRequest { code: "styler::style_file('C:/Users/zdw12/AppData/Local/Temp/styler-2df9a4f1-2db3-452f-907d-86a7bcee1826.R')", silent: true, store_history: false, user_expressions: Object {}, allow_stdin: true, stop_on_error: false } }
[R]     at crates\amalthea\src\socket\shell.rs:185
[R] 
[R]   2024-11-29T00:59:59.332295Z  INFO  Sending message to UI comm: Event(Busy(BusyParams { busy: true }))
[R]     at crates\ark\src\ui\sender.rs:50
[R] 

Question 2

• Running the command R: New R File performs as expected, creating a new R file
  

• Running the task R: Render document with R Markdown using the following drop-down option when an R markdown file is loaded and it renders as expected.
  

Question 3

As suggested, I turned off the Positron Kernel Supervisor: Enable option, but the formatting issues remain. Below is the debug output I get when I run formatting for a chunk (Ctrl+K Ctrl+F) and the Ctrl + Shift + A still doesn't work.

[R]   2024-11-29T01:20:56.753858Z  INFO  Received shell notification: JupyterMessage { zmq_identities: [[112, 111, 115, 105, 116, 114, 111, 110, 45, 115, 104, 101, 108, 108]], header: JupyterHeader { msg_id: "0949ad50-0efe-4fde-913e-423dfc283f2a", session: "146a802c014a28496c3345a88127fc6f", username: "zdw12", date: "2024-11-29T01:20:56.752Z", msg_type: "comm_msg", version: "5.0" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-1-37fb16b6", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("packageVersion"), "params": Array [String("styler"), Null]}} } }
[R]     at crates\amalthea\src\socket\shell.rs:232
[R] 
[R]   2024-11-29T01:20:56.762556Z  INFO  Received shell request: JupyterMessage { zmq_identities: [[112, 111, 115, 105, 116, 114, 111, 110, 45, 115, 104, 101, 108, 108]], header: JupyterHeader { msg_id: "d69e645e-cc4e-4440-be2f-cd534e5b8d2b", session: "146a802c014a28496c3345a88127fc6f", username: "zdw12", date: "2024-11-29T01:20:56.761Z", msg_type: "execute_request", version: "5.0" }, parent_header: None, content: ExecuteRequest { code: "styler::style_file('C:/Users/zdw12/AppData/Local/Temp/styler-3c6d3a54-3dbf-48fa-bb08-62a710df89ae.R')", silent: true, store_history: false, user_expressions: Object {}, allow_stdin: false, stop_on_error: false } }
[R]     at crates\amalthea\src\socket\shell.rs:185

[strengejacke]

I'm not sure if my keyboard shortcut is recognized at all? I can't "format selection", only the document, which then pop ups the window saying no formatter is installed. Ctrl+Shift+A doesn't do anything.

When I press Ctrl+K, Ctrl+F, it says:

Although this is supposed to happen:

Question 2: Creating new R files and rendering R markdown works

Question 3: yes, still nothing happens

Question 1: I tried Ctrl+Shift+A, Ctrl+K & Ctrl+F, and Shift+Alt+A, output did not change:

Here's my settings file:

{
  // this is the settings.json file

  // file behaviour
  "files.hotExit": "onExitAndWindowClose",
  "files.defaultLanguage": "r",
  "files.insertFinalNewline": true,
  "files.trimFinalNewlines": true,
  "files.trimTrailingWhitespace": true,
  "positron.r.diagnostics.enable": false,
  "positron.r.kernel.logLevel": "debug",
  "positronKernelSupervisor.enable": false,

  // editor settings
  "editor.fontFamily": "'Fira Code', Consolas, 'Courier New', monospace",
  "editor.fontLigatures": true,
  "editor.guides.bracketPairs": "active",
  "editor.guides.indentation": false,
  "editor.cursorBlinking": "phase",
  "editor.renderWhitespace": "trailing",
  "editor.defaultFormatter": "positron.positron-r",
  "editor.formatOnType": true,
  "editor.rulers": [
    {
      "column": 80,
      "color": "#5a5a5a80"
    }, // right rule
    {
      "column": 95,
      "color": "#5a5a5a30"
    }, // right rule
    {
      "column": 120,
      "color": "#5a5a5a40"
    } // extra right rule
  ],
  "application.experimental.positronPlotsEditor": true,

  // todo tree
  "todo-tree.highlights.customHighlight": {
    "TODO": {
      "background": "#F5910044",
      "foreground": "#fffc00FF"
    },
    "BUG": {
      "icon": "bug",
      "background": "#D3262655",
      "foreground": "#FF3300FF"
    },
    "HACK": {
      "icon": "tools"
    },
    "FIXME": {
      "icon": "flame",
      "background": "#00996844",
      "foreground": "#25D366FF"
    }
  },

  // git settings
  "git.autofetch": true,
  "git.confirmSync": false,
  "git.suggestSmartCommit": false,

  // github settings
  "githubPullRequests.fileListLayout": "tree",
  "githubPullRequests.defaultMergeMethod": "squash",
  "githubPullRequests.pullBranch": "never",
  "githubIssues.queries": [
    {
      "label": "My Issues",
      "query": "is:open assignee:${user} repo:${owner}/${repository}",
      "groupBy": [
        "milestone"
      ]
    },
    {
      "label": "Created Issues",
      "query": "author:${user} state:open repo:${owner}/${repository} sort:created-desc"
    },
    {
      "label": "Recent Issues",
      "query": "state:open repo:${owner}/${repository} sort:created-desc"
    }
  ],

  // Codesnap
  "codesnap.boxShadow": "rgba(0, 0, 0, 0.55) 0px 20px 60px",
  "codesnap.backgroundColor": "#6090a0",
  "codesnap.containerPadding": "1em",
  "codesnap.showWindowControls": false,
  "codesnap.shutterAction": "copy",

  // Wrap at 80 columns with the "Rewrap" extension
  "rewrap.wrappingColumn": 80,

  // Debugger
  "debug.toolBarLocation": "docked",
  "chatgpt.lang": "en",
  "workbench.colorTheme": "Default Positron Dark"
}

[juliasilge]

@zwallen Can you share if you can format regular .R files? Your problem with Quarto may be different, and it looks from your logs like the kernel is successfully formatting... something.

[juliasilge]

@strengejacke and @lijiaqi-github are you all working with an untitled .R file or an .R file that is saved to disk?

[strengejacke]

It seems to work for saved files, despite the indention is not correct. In this video, I edited the script (removed whitespace around =), saved the file and pressed ctrl+shift+A. After that, I pushed "tab" to correct indention.

format.mp4

For unsaved files, nothing happens.

[lijiaqi-github]

@strengejacke and @lijiaqi-github are you all working with an untitled .R file or an .R file that is saved to disk?

Yes, I tested this in a new unsaved R file, Like @strengejacke said, formatting in a saved file seems to work.

[juliasilge]

Ah gotcha, OK! It's quite a coincidence that we have had multiple folks run into this at once, but yep, currently the styler-based formatter only works on "real" files, not on untitled files that have never been saved to disk. This is currently as expected.

We have some MAJOR improvements in formatting coming along shortly, so I don't think we're going to put much more effort into our stopgap solution using styler in the meantime. Thank you so much for the reports, and keep your eyes open for some major steps forward in R formatting soon! 🙌