Not recognising R interpreter #3832

skthewimp · 2024-07-03T05:06:38Z

Positron Version:

Steps to reproduce the issue:

Open an R file
Hit "run code"

What did you expect to happen?

The code to be run. Nothing happened. If I look at the interpreters on the top right, I only see Python, no R interpreters there. I've been using RStudio on my machine (with R 4.4.1) for a very long time now

Were there any error messages in the output or Developer Tools console?

No

lionel- · 2024-07-03T08:27:41Z

Can you provide us with the Positron Extension log please? See #3791 (comment).

skthewimp · 2024-07-03T08:31:21Z

2024-07-03 13:25:18.526 [info] Log level: Debug
2024-07-03 13:25:18.526 [info] Refreshing testthat status
2024-07-03 13:25:18.526 [info] Not working in an R package
2024-07-03 13:25:18.526 [info] Context key 'testthatIsConfigured' is 'false'
2024-07-03 13:25:18.526 [info] Context key 'testthatHasTests' is 'false'

lionel- · 2024-07-03T08:32:36Z

Can you provide the complete log please?

skthewimp · 2024-07-03T09:12:42Z

this is all i can see. how can i find the complete log?

lionel- · 2024-07-03T10:36:24Z

Gotcha! What's your operating system? Where is R installed on your machine and how did you install it?

skthewimp · 2024-07-03T10:41:30Z

MacOS

/usr/local/bin/R

downloaded from the website (in fact after this i reinstalled and upgraded ot the latest version (4.4.1) )
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

jennybc · 2024-07-03T15:07:29Z

When you say "downloaded from the website", I assume you mean CRAN. Can you confirm? From the "Download and Install R" section of https://cran.r-project.org/.

Can you use R in the terminal? In RStudio? If so, what does R.home() show you in those contexts?

skthewimp · 2024-07-04T04:41:41Z

Yes i can use everywhere. and I got it from cran

R.home() shows "/Library/Frameworks/R.framework/Resources"

jennybc · 2024-07-04T05:03:01Z

Hmm, that's pretty surprising that the log just ends there 🤔

Maybe the developer tools is the next best place to look for info. How to access this is described in #3707 (reply in thread).

jennybc · 2024-07-04T05:08:49Z

Can you also paste the content from Positron > About Positron, please?

For example, mine looks like:

Positron Version: 2024.06.1 (Universal) build 54
Code - OSS Version: 1.90.0
Commit: 5115c73e0670f39139e55eeedf0717b468a0658d
Date: 2024-07-03T03:51:33.756Z
Electron: 29.4.0
Chromium: 122.0.6261.156
Node.js: 20.9.0
V8: 12.2.281.27-electron.0
OS: Darwin arm64 22.6.0

jennybc · 2024-07-04T05:11:01Z

And also show the result of R.version when you successfully run it through other means. Output will be something like this:

R.version
#>                _                           
#> platform       aarch64-apple-darwin20      
#> arch           aarch64                     
#> os             darwin20                    
#> system         aarch64, darwin20           
#> status                                     
#> major          4                           
#> minor          4.0                         
#> year           2024                        
#> month          04                          
#> day            24                          
#> svn rev        86474                       
#> language       R                           
#> version.string R version 4.4.0 (2024-04-24)
#> nickname       Puppy Cup

^{Created on 2024-07-03 with reprex v2.0.2}

skthewimp · 2024-07-04T05:21:58Z

Positron Version: 2024.06.1 (Universal) build 54
Code - OSS Version: 1.90.0
Commit: 5115c73
Date: 2024-07-03T03:51:33.756Z
Electron: 29.4.0
Chromium: 122.0.6261.156
Node.js: 20.9.0
V8: 12.2.281.27-electron.0
OS: Darwin arm64 23.5.0

skthewimp · 2024-07-04T05:22:23Z

platform aarch64-apple-darwin20
arch aarch64
os darwin20
system aarch64, darwin20
status
major 4
minor 4.1
year 2024
month 06
day 14
svn rev 86737
language R
version.string R version 4.4.1 (2024-06-14)
nickname Race for Your Life

skthewimp · 2024-07-04T05:24:05Z

I added this "/Library/Frameworks/R.framework/Resources" to my path, and now Positron is able to see the R interpreter.

however, i'm getting a new error now there (I've never had a problem on RStudio, btw. continues to work beautifully there)

Error: Socket connect timed out after 20 seconds
/usr/local/bin/R --connection_file /var/folders/v8/6twm3vf51cj3s4zz2c1v8pqr0000gn/T/kernel-JOwa4U/connection.json --log /var/folders/v8/6twm3vf51cj3s4zz2c1v8pqr0000gn/T/kernel-JOwa4U/kernel.log --startup-file /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/scripts/startup.R --session-mode console --startup-notifier-file /var/folders/v8/6twm3vf51cj3s4zz2c1v8pqr0000gn/T-JupyterDelayStartupTd0tTq/file -- --interactive --no-restore-data
WARNING: unknown option '--connection_file'

ARGUMENT '/var/folders/v8/6twm3vf51cj3s4zz2c1v8pqr0000gn/T/kernel-JOwa4U/connection.json' __ignored__

WARNING: unknown option '--log'

ARGUMENT '/var/folders/v8/6twm3vf51cj3s4zz2c1v8pqr0000gn/T/kernel-JOwa4U/kernel.log' __ignored__

WARNING: unknown option '--startup-file'

ARGUMENT '/Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/scripts/startup.R' __ignored__

WARNING: unknown option '--session-mode'

ARGUMENT 'console' __ignored__

WARNING: unknown option '--startup-notifier-file'

ARGUMENT '/var/folders/v8/6twm3vf51cj3s4zz2c1v8pqr0000gn/T-JupyterDelayStartupTd0tTq/file' __ignored__

WARNING: unknown option '--'

skthewimp · 2024-07-04T05:57:05Z

and the log:

2024-07-04 11:18:38.901 [info] Log level: Debug
2024-07-04 11:18:38.901 [info] Refreshing testthat status
2024-07-04 11:18:38.901 [info] Not working in an R package
2024-07-04 11:18:38.901 [info] Context key 'testthatIsConfigured' is 'false'
2024-07-04 11:18:38.901 [info] Context key 'testthatHasTests' is 'false'
2024-07-04 11:18:39.951 [info] Resolved R binary at /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/bin/R
2024-07-04 11:18:39.953 [info] Candidate R binary at /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/bin/R
2024-07-04 11:18:39.953 [info] R installation discovered: {
  "valid": true,
  "supported": true,
  "binpath": "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/bin/R",
  "homepath": "/Library/Frameworks/R.framework/Resources",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.4.1",
    "major": 4,
    "minor": 4,
    "patch": 1,
    "prerelease": [],
    "build": [],
    "version": "4.4.1"
  },
  "version": "4.4.1",
  "arch": "arm64",
  "current": true,
  "orthogonal": false
}
2024-07-04 11:18:39.953 [info] Candidate R binary at /Library/Frameworks/R.framework/Versions/4.1/Resources/bin/R
2024-07-04 11:18:39.953 [info] R installation discovered: {
  "valid": true,
  "supported": true,
  "binpath": "/Library/Frameworks/R.framework/Versions/4.1/Resources/bin/R",
  "homepath": "/Library/Frameworks/R.framework/Resources",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.4.1",
    "major": 4,
    "minor": 4,
    "patch": 1,
    "prerelease": [],
    "build": [],
    "version": "4.4.1"
  },
  "version": "4.4.1",
  "arch": "arm64",
  "current": false,
  "orthogonal": false
}
2024-07-04 11:18:39.953 [info] Filtering out /Library/Frameworks/R.framework/Versions/4.1/Resources/bin/R: not current and also not orthogonal.
2024-07-04 11:18:39.954 [info] Resolved R binary at /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/bin/R
2024-07-04 11:18:39.954 [info] Candidate R binary at /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/bin/R
2024-07-04 11:18:39.954 [info] R installation discovered: {
  "valid": true,
  "supported": true,
  "binpath": "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/bin/R",
  "homepath": "/Library/Frameworks/R.framework/Resources",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.4.1",
    "major": 4,
    "minor": 4,
    "patch": 1,
    "prerelease": [],
    "build": [],
    "version": "4.4.1"
  },
  "version": "4.4.1",
  "arch": "arm64",
  "current": true,
  "orthogonal": false
}

jennybc · 2024-07-05T14:36:28Z

I think this got buried by my other requests. I still think it would be useful to get a look at the developer tools.

Maybe the developer tools is the next best place to look for info. How to access this is described in #3707 (reply in thread).

Update: maybe that's where the snippet in #3832 (comment) came from? Can you confirm?

jennybc · 2024-07-05T15:17:30Z

Jotting down a few notes mostly to myself: I find it odd that adding "/Library/Frameworks/R.framework/Resources" to the PATH unblocked discovery of multiple R versions (vs. just the current version). I tend to think there is something intermittent happening that ?perhaps causes a timing problem / delay? and that some random positive event coincided with modifying the PATH, i.e. that that is a red herring. Because this log looks completely normal to me now: #3832 (comment). Is the "Error: Socket connect timed out after 20 seconds" the real thread to pursue?

jennybc · 2024-07-05T18:04:52Z

More observations:

Error: Socket connect timed out after 20 seconds
/usr/local/bin/R --connection_file .... <lots of warnings about unknown options>

The equivalent log for me shows:

[R] /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/ark/ark --connection_file /var/folders/zb/yzf8zvwd4p1dq8q3bfjz4tt80000gp/T/kernel-NdoQjM/connection.json --log /var/folders/zb/yzf8zvwd4p1dq8q3bfjz4tt80000gp/T/kernel-NdoQjM/kernel.log --startup-file /Applications/Positron.app/Contents/Resources/app/extensions/positron-r/resources/scripts/startup.R --session-mode console -- --interactive --no-restore-data

Can you do ls -al /usr/local/bin/R? I see

~/rrr/positron % ls -al /usr/local/bin/R
lrwxr-xr-x  1 root  admin  47  3 May 07:55 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R

I.e. the R there is a symlink pointing at an actual R binary (via another symlink). From some of your output, it feels like this may not be true for you?

FWIW I highly recommend managing one's R installations via rig, if you are open to that: https://github.com/r-lib/rig. If you intend to have more than 1 R installation that is usable, you almost have to do that.

jennybc · 2024-07-05T18:54:10Z

Have you done anything with this bit of configuration re: the Ark kernel (Positron > R > Kernel: Path)? If so, what? It should be unset for a typical user.

skthewimp · 2024-07-08T04:52:35Z

Phew! that was it! While my system wasn't able to locate the interpreter, I had assumed this is where you set the path, and i ahd put somethign there.

Now, FINALLY, it's all working for me! Thanks so much for all the support.

Intent: Avoid confusion such as in #3832 where a user thought the path for Ark was the path for R. - Add a note that path to Ark is not path to R - Split advanced settings into a separate section. This way the most useful user settings are separated from the dev or debug settings and are easier for users to skim through. It might also give pause before trying adanced settings like the path to Ark. https://github.com/posit-dev/positron/assets/4465050/669161e2-3d54-4e9e-8a36-9c25fe39781a

skthewimp added the bug Something isn't working label Jul 3, 2024

lionel- added the lang: r label Jul 3, 2024

skthewimp closed this as completed Jul 3, 2024

skthewimp reopened this Jul 3, 2024

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petetronic added the support label Jul 7, 2024

skthewimp closed this as completed Jul 8, 2024

lionel- mentioned this issue Jul 10, 2024

Split R settings in two sections #3950

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Not recognising R interpreter #3832

Not recognising R interpreter #3832

skthewimp commented Jul 3, 2024

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skthewimp commented Jul 8, 2024

Not recognising R interpreter #3832

Not recognising R interpreter #3832

Comments

skthewimp commented Jul 3, 2024

Positron Version:

Steps to reproduce the issue:

What did you expect to happen?

Were there any error messages in the output or Developer Tools console?

lionel- commented Jul 3, 2024

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