'R path not working: /usr/local/bin/R (Can be changed in setting r.rpath.XXX)'

[tvqt]

Description
R Debugger doesn't see the R executable, even though the correct R path has been given?

To Reproduce

1. Install the prerequisites (R, VSCode, the R extension for VSCode)
2. Install R Debugger, along with dependencies
3. Create a new folder, with a simple R file, test.R, with something like below
4. Try to run said code

Your R code

test.R

print(hello world')
a <- 2 + 2

Your Launch config
If applicable, the launch config that causes the bug. E.g.:

        {
    // Use IntelliSense to learn about possible attributes.
    // Hover to view descriptions of existing attributes.
    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
    "version": "0.2.0",
    "configurations": [
        {
            "type": "R-Debugger",
            "name": "Launch R-Workspace",
            "request": "launch",
            "debugMode": "workspace",
            "workingDirectory": "${workspaceFolder}"
        },
        {
            "type": "R-Debugger",
            "name": "Debug R-File",
            "request": "launch",
            "debugMode": "file",
            "workingDirectory": "${workspaceFolder}",
            "file": "${file}"
        },
        {
            "type": "R-Debugger",
            "name": "Debug R-Function",
            "request": "launch",
            "debugMode": "function",
            "workingDirectory": "${workspaceFolder}",
            "file": "${file}",
            "mainFunction": "main",
            "allowGlobalDebugging": false
        },
        {
            "type": "R-Debugger",
            "name": "Debug R-Package",
            "request": "launch",
            "debugMode": "workspace",
            "workingDirectory": "${workspaceFolder}",
            "includePackageScopes": true,
            "loadPackages": [
                "."
            ]
        },
        {
            "type": "R-Debugger",
            "request": "attach",
            "name": "Attach to R process",
            "splitOverwrittenOutput": true
        }
    ]
}

Expected behavior
Run

Actual behavior
Throws an error

Desktop (please complete the following information):

• OS: Mac OS 12.0 (M1 based)
• R Version: R version 4.1.2 (2021-11-01) -- "Bird Hippie"
• vscDebugger Version: vscDebugger_0.4.7
• vscode-r-debugger Version: v0.4.7

Additional context
I'm new to VS Code, coming from RStudio, so I may have messed something up here, however, I've tried installing it three times now (reinstalling VSCode, with no luck!). Don't know what I'm doing wrong.

The path to R is the one in the title, I've double checked! I've added the path to both the rterm and rpath options in settings, and it doesn't work, nor does removing both. VS Code can see the R binary for the terminal, but the debugger seemingly cannot see it

[ManuelHentschel]

Maybe the R start up takes unusually long? You can change the config "r.debugger.timeouts.startup": 2000 to wait longer for R to get ready.

[aldencabajar]

Maybe the R start up takes unusually long? You can change the config "r.debugger.timeouts.startup": 2000 to wait longer for R to get ready.

Got the same error too. Increasing the timeout startup setting works.

[wjones127]

I was having this problem as well (same OS and R version) and increasing the timeout startup setting did not work in my case. I ran the extension in debug mode and threw a breakpoint here:

VSCode-R-Debugger/src/debugRuntime.ts

Line 166 in d413046

await this.rSessionStartup.wait(this.startupTimeout);

I could see that this.rSession.cp.pid indeed had a valid R session and that it was alive in Activity Monitor. However, even after a couple minutes of waiting I get that error.

I added some breakpoints at the stdout and stderr handlers but they never seem to be hit. So just not getting any response from the R session.

In addition, I am able to get it to run with the default attach configuration. (Followed instruction here: https://github.com/ManuelHentschel/VSCode-R-Debugger#attach-mode)

Any suggestions for where to check? I'm happy to help debug further.

[xiajunwen1007]

I have the same issue.

[THargreaves]

I'm having the same issue, also with M1 MacBook. Increasing the startup timeout had no effect.

[ManuelHentschel]

Can you please post the content of the output channel (strl+shift+u by default) named "R Debugger"?

[wjones127]

Sure. Here is testing with default settings:

[info....] [21:28:34.255] [ ] Custom server listening on localhost:55002
[info....] [21:28:34.297] [ ] Request handled in VS Code:
[info....] [21:28:34.297] [ ] {"command":"initialize","arguments":{"clientID":"vscode","clientName":"Visual Studio Code","adapterID":"R-Debugger","pathFormat":"path","linesStartAt1":true,"columnsStartAt1":true,"supportsVariableType":true,"supportsVariablePaging":true,"supportsRunInTerminalRequest":true,"locale":"en-us","supportsProgressReporting":true,"supportsInvalidatedEvent":true,"supportsMemoryReferences":true,"threadId":1,"extensionVersion":"0.4.7","rStrings":{"prompt":"<#v\\s\\c>","continue":"<##v\\s\\c>","startup":"<v\\s\\c\\R\\STARTUP>","libraryNotFound":"<v\\s\\c\\LIBRARY\\NOT\\FOUND>","packageName":"vscDebugger"}},"type":"request","seq":1}
[info....] [21:28:34.297] [ ] R Startup:
[info....] [21:28:34.297] [ ] {"path":"/usr/local/bin/R","args":["--quiet","--no-save","--interactive"],"cwd":"/Users/willjones/Documents/VSCode-R-Debugger/test/R"}
[stdin...] [21:28:38.795] [n] base::cat("<v\\s\\c\\R\\STARTUP>\n")
[error...] [21:29:00.269] [n] R path not working:
[error...] [21:29:00.269] [n] /usr/local/bin/R
[error...] [21:29:00.269] [ ] (Can be changed in setting r.rpath.XXX)
[cpinfo..] [21:29:00.322] [ ] sending signal SIGKILL...
[cpinfo..] [21:29:00.323] [ ] sent signal
[cpinfo..] [21:29:00.342] [ ] Child process exited with code: null
[stdin...] [21:29:00.368] [n] vscDebugger::.vsc.handleJson(json="{\"command\":\"disconnect\",\"arguments\":{\"restart\":false},\"type\":\"request\",\"seq\":2}")
[cpinfo..] [21:29:00.831] [ ] sending signal SIGKILL...
[cpinfo..] [21:29:00.833] [ ] sent signal
[info....] [21:29:20.373] [ ] Killing R...
[cpinfo..] [21:29:20.373] [ ] sending signal SIGKILL...
[cpinfo..] [21:29:20.377] [ ] sent signal

One thing I notice is that /usr/local/bin/R is a symlink to /Library/Frameworks/R.framework/Resources/bin/R on Mac. And that file is a shell script, not a binary. I believe this is the corresponding source code. It sets up several environment variables and then runs the executable at /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/bin/exec/R (notice the exec directory near the end of the path).

When I set that executable as r.rpath.mac, here's the output from R Debugger:

[info....] [21:41:09.519] [ ] Request handled in VS Code:
[info....] [21:41:09.519] [ ] {"command":"initialize","arguments":{"clientID":"vscode","clientName":"Visual Studio Code","adapterID":"R-Debugger","pathFormat":"path","linesStartAt1":true,"columnsStartAt1":true,"supportsVariableType":true,"supportsVariablePaging":true,"supportsRunInTerminalRequest":true,"locale":"en-us","supportsProgressReporting":true,"supportsInvalidatedEvent":true,"supportsMemoryReferences":true,"threadId":1,"extensionVersion":"0.4.7","rStrings":{"prompt":"<#v\\s\\c>","continue":"<##v\\s\\c>","startup":"<v\\s\\c\\R\\STARTUP>","libraryNotFound":"<v\\s\\c\\LIBRARY\\NOT\\FOUND>","packageName":"vscDebugger"}},"type":"request","seq":1}
[info....] [21:41:09.520] [ ] R Startup:
[info....] [21:41:09.520] [ ] {"path":"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/bin/exec/R","args":["--quiet","--no-save","--interactive"],"cwd":"/Users/willjones/Documents/VSCode-R-Debugger/test/R"}
[stdin...] [21:41:12.791] [n] base::cat("<v\\s\\c\\R\\STARTUP>\n")
[stdout..] [21:41:13.856] [n] Fatal error: R home directory is not defined
[cpinfo..] [21:41:15.454] [ ] Child process exited with code: 2
[error...] [21:41:33.857] [n] R path not working:
[error...] [21:41:33.857] [n] /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/bin/exec/R
[error...] [21:41:33.857] [ ] (Can be changed in setting r.rpath.XXX)
[cpinfo..] [21:41:33.908] [ ] process already exited with code 2
[stdin...] [21:41:33.928] [n] vscDebugger::.vsc.handleJson(json="{\"command\":\"disconnect\",\"arguments\":{\"restart\":false},\"type\":\"request\",\"seq\":2}")
[cpinfo..] [21:41:34.416] [ ] process already exited with code 2

Running that binary directly from the shell also gives a similar error message: "Fatal error: R home directory is not defined".

So my conclusions so far is that we need a way to start the R process from the shell script, but then identify the correct binary to attach to later. Does that seem right?

[tvqt]

I seemed to have fixed it, but honestly, I have no clue how- I uninstalled R, the debugger, the Visual Studio Code extension, and reinstalled them a couple of times- the first time, I got new errors, however the second time, it all worked okay. Seemingly random, and not very useful, but glad to get it working nonetheless 😅 it might have something to do with installing via homebrew versus installing with a pkg downloaded from R's website maybe?

As with @THargreaves, before doing the above, I had tried increasing the timeout a bunch of times, to larger and larger numbers, but none of them worked.

[wjones127]

Nevermind about the shell vs executable idea. I tested on an Intel Mac (OSX 11.6, R 4.0.2) and it works just fine with default settings. I'll do some more testing to see what's different on the M1 mac vs Intel and post what I find.

For comparison, here's the successful log output:

[info....] [22:02:10.618] [ ] Request handled in VS Code:
[info....] [22:02:10.618] [ ] {"command":"initialize","arguments":{"clientID":"vscode","clientName":"Visual Studio Code","adapterID":"R-Debugger","pathFormat":"path","linesStartAt1":true,"columnsStartAt1":true,"supportsVariableType":true,"supportsVariablePaging":true,"supportsRunInTerminalRequest":true,"locale":"en-us","supportsProgressReporting":true,"supportsInvalidatedEvent":true,"supportsMemoryReferences":true,"threadId":1,"extensionVersion":"0.4.7","rStrings":{"prompt":"<#v\\s\\c>","continue":"<##v\\s\\c>","startup":"<v\\s\\c\\R\\STARTUP>","libraryNotFound":"<v\\s\\c\\LIBRARY\\NOT\\FOUND>","packageName":"vscDebugger"}},"type":"request","seq":1}
[info....] [22:02:10.619] [ ] R Startup:
[info....] [22:02:10.619] [ ] {"path":"/usr/local/bin/R","args":["--quiet","--no-save","--interactive"],"cwd":"/Users/willjones/Documents/code_projects/VSCode-R-Debugger/test/R"}
[stdout..] [22:02:10.832] [ ] > 
[stdin...] [22:02:12.622] [n] base::cat("<v\\s\\c\\R\\STARTUP>\n")
[stdout..] [22:02:12.625] [n] <v\s\c\R\STARTUP>
[info....] [22:02:12.626] [ ] R Session ready
[stdin...] [22:02:12.628] [n] base::tryCatch(expr=base::library(vscDebugger), error=function(e) base::cat("<v\\s\\c\\LIBRARY\\NOT\\FOUND>\n"))
[info....] [22:02:12.628] [ ] Initialize Arguments:
[info....] [22:02:12.629] [ ] {"clientID":"vscode","clientName":"Visual Studio Code","adapterID":"R-Debugger","pathFormat":"path","linesStartAt1":true,"columnsStartAt1":true,"supportsVariableType":true,"supportsVariablePaging":true,"supportsRunInTerminalRequest":true,"locale":"en-us","supportsProgressReporting":true,"supportsInvalidatedEvent":true,"supportsMemoryReferences":true,"threadId":1,"extensionVersion":"0.4.7","rStrings":{"prompt":"<#v\\s\\c>","continue":"<##v\\s\\c>","startup":"<v\\s\\c\\R\\STARTUP>","libraryNotFound":"<v\\s\\c\\LIBRARY\\NOT\\FOUND>","packageName":"vscDebugger"},"useJsonSocket":true,"jsonHost":"localhost","jsonPort":58160,"useSinkSocket":true,"sinkHost":"localhost","sinkPort":58159}
[stdin...] [22:02:12.629] [n] vscDebugger::.vsc.handleJson(json="{\"command\":\"initialize\",\"arguments\":{\"clientID\":\"vscode\",\"clientName\":\"Visual Studio Code\",\"adapterID\":\"R-Debugger\",\"pathFormat\":\"path\",\"linesStartAt1\":true,\"columnsStartAt1\":true,\"supportsVariableType\":true,\"supportsVariablePaging\":true,\"supportsRunInTerminalRequest\":true,\"locale\":\"en-us\",\"supportsProgressReporting\":true,\"supportsInvalidatedEvent\":true,\"supportsMemoryReferences\":true,\"threadId\":1,\"extensionVersion\":\"0.4.7\",\"rStrings\":{\"prompt\":\"<#v\\\\s\\\\c>\",\"continue\":\"<##v\\\\s\\\\c>\",\"startup\":\"<v\\\\s\\\\c\\\\R\\\\STARTUP>\",\"libraryNotFound\":\"<v\\\\s\\\\c\\\\LIBRARY\\\\NOT\\\\FOUND>\",\"packageName\":\"vscDebugger\"},\"useJsonSocket\":true,\"jsonHost\":\"localhost\",\"jsonPort\":58160,\"useSinkSocket\":true,\"sinkHost\":\"localhost\",\"sinkPort\":58159},\"type\":\"request\",\"seq\":1}")
[stdout..] [22:02:12.629] [ ] > 

[ManuelHentschel]

Thanks for the logs!

I don't have a mac available, so I can't really debug this any further, but a quick google search seems to indicate that you are not the only one having problems with R and M1. So I'd hope that some of the future R updates (or node/vscode/whatever) fixes this, if not I'll have to try and get my hands on a mac...

I noticed that the shell script you linked seems to check the cpu architecture to some extent, but no idea if that has any effect in this case. If you want to play around a bit to get the binary working, you could also try setting relevant environment variables yourself, using the "env" entry in your launch config.

[xiajunwen1007]

It seems like vscdebugger doesn't support arm64. Maybe it is caused by this reason?

[totoroyyb]

@xiajunwen1007 I don't think the build architecture of vscdebugger is the root cause. I've tried to compile an arm64 native version of vscdebugger on my m1 mbp and now vscdebugger can be loaded correctly. However, the VS Code still throws me the same error saying cannot find the R executable.

[totoroyyb]

After spending one day investigating this issue, I noticed one thing on the arm64 build of the R executable for macOS M1 chip, version 4.1.2 (potentially a bug). The arm64 build seems to have some trouble picking up the data piped in when the --interactive flag is passed.

For example, try to run the following command:

echo "base::cat('Hello\\\\n')\\n" | R --no-save --interactive > test.txt

And when you examine the test.txt file, you will find no output here.

I've tested on the intel build (4.1.2), and I can get the expected behavior with a valid output.

Could anyone maybe confirm the issue?

[eitsupi]

It seems the same output. (I've tested on Docker containers on amd64 WSL2 and arm64 Raspberry Pi 4)

$ echo "base::cat('Hello\\\\n')\\n" | R --no-save --interactive > /tmp/test.txt
Error: unexpected '\\' in "base::cat('Hello\\n')\"
$ ls /tmp/
test.txt
$ cat /tmp/test.txt

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> base::cat('Hello\\n')\n
>

$ echo "base::cat('Hello\\\\n')\\n" | R --no-save --interactive > /tmp/test.txt
Error: unexpected '\\' in "base::cat('Hello\\n')\"
$ ls /tmp/
test.txt
$ cat /tmp/test.txt

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> base::cat('Hello\\n')\n
>

[totoroyyb]

@eitsupi Sorry, I didn't mention I was referring to the build for the macOS M1 chip. I guess this issue is specific for the macOS M1 arm64 build instead of all arm64 builds.

Also, it seems macOS takes the strings (with escaping) in a different way.

echo "base::cat('Hello\\\\n')\\n"

I am using zsh with echo, and it can correctly feed this line to the R console without any warning like Error: unexpected '\\' in "base::cat('Hello\\n')\"