Shinylive-R embedded in Quarto not rendering without R in PATH

[kv9898]

I was asked to file it here by the Quarto team (quarto-dev/quarto#557).

System details:

Windows 11 64-bit

Version details:

Positron Version: 2024.09.0 (system setup) build 77
Code - OSS Version: 1.93.0
Date: 2024-09-23T02:44:07.418Z
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 10.0.22631

Quarto: 1.6.15
shinylive (R package): 0.2.0

Interpreter details:

R 4.4.1

Describe the issue:

Seems to be a Windows only issue.

In a nutshell, without R in PATH for Windows:

• Positron/VS Code + Quarto + Shinylive + R = ×
• Positron/VS Code + Quarto + Shinylive + Python = √
• RStudio + Quarto + Shinylive + R = √
• Positron/VS Code + Shiny + R = √

Steps to reproduce the issue:

0. No R in PATH (default setting for Windows)
1. Start a new folder for the Quarto project
2. Open the folder in Positron/VS Code
3. Execute quarto add quarto-ext/shinylive in Terminal to install the Quarto extension.
4. Run install.packages("shinylive") if it has not been installed before.
5. Start a .qmd file
6. Include the following minimum quarto document, and render:

---
title: "Shinylive R test"
filters:
  - shinylive
---
```{shinylive-r}
#| standalone: true

```

7. You get an error.

Expected or desired behavior:

Running normally as in RStudio.

From RStudio Background Jobs:

==> quarto preview shinyliver.qmd --to default --no-watch-inputs --no-browse

pandoc 
  to: html
  output-file: shinyliver.html
  standalone: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  title: Shinylive R test
  
ℹ Loading metadata database
✔ Loading metadata database ... done

Output created: shinyliver.html

Watching files for changes
Browse at http://localhost:5239/

Were there any error messages in the UI, Output panel, or Developer Tools console?

From Positron/VS Code Terminal:

PS D:\OneDrive - London School of Economics\Desktop\shinyliveRError> quarto preview "d:/OneDrive - London School of Economics/Desktop/shinyliveRError/shinyliver.qmd" --no-browser --no-watch-inputs
pandoc 
  to: html
  output-file: shinyliver.html
  standalone: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  title: Shinylive R test

(E) Error running 'Rscript' command. Perhaps you need to install / update the 'shinylive' R package?
 Error:
 PandocError {}
Error running filter D:/quarto/share/filters/main.lua:
...iveRError\_extensions\quarto-ext\shinylive\shinylive.lua:40: Error running 'Rscript' command. Perhaps you need to install / update the 'shinylive' R package?

stack traceback:
        ...iveRError\_extensions\quarto-ext\shinylive\shinylive.lua:40: in global 'throw_quarto_error'
        ...iveRError\_extensions\quarto-ext\shinylive\shinylive.lua:86: in global 'callRShinylive'
        ...iveRError\_extensions\quarto-ext\shinylive\shinylive.lua:113: in global 'callShinylive'
        ...iveRError\_extensions\quarto-ext\shinylive\shinylive.lua:286: in global 'ensureBaseSetup'
        ...iveRError\_extensions\quarto-ext\shinylive\shinylive.lua:315: in global 'ensureLanguageSetup'
        ...iveRError\_extensions\quarto-ext\shinylive\shinylive.lua:424: in function <...iveRError\_extensions\quarto-ext\shinylive\shinylive.lua:408>        
        [C]: in ?
        [C]: in method 'walk'
        D:/quarto/share/filters/main.lua:558: in local 'checked_walk'
        D:/quarto/share/filters/main.lua:610: in function 'run_emulated_filter'
        D:/quarto/share/filters/main.lua:1335: in local 'callback'
        [string "..."]:1888: in field 'withScriptFile'
        D:/quarto/share/filters/main.lua:1351: in upvalue 'run_emulated_filter_chain'
        D:/quarto/share/filters/main.lua:1389: in function <D:/quarto/share/filters/main.lua:1386>
stack traceback:
        D:/quarto/share/filters/main.lua:558: in local 'checked_walk'
        D:/quarto/share/filters/main.lua:610: in function 'run_emulated_filter'
        D:/quarto/share/filters/main.lua:1335: in local 'callback'
        [string "..."]:1888: in field 'withScriptFile'
        D:/quarto/share/filters/main.lua:1351: in upvalue 'run_emulated_filter_chain'
        D:/quarto/share/filters/main.lua:1389: in function <D:/quarto/share/filters/main.lua:1386>

This error is misleading since it tells the user to (re)install the shinylive R package, whereas what the user really needs to to is to put R in PATH/the lua should detect R in other ways.

@jennybc points out in quarto-dev/quarto#557 (comment) that:

I can speak to the Positron + Windows part of this. By default, the CRAN R installer for Windows does not put R on the PATH. Therefore R installation discovery focuses on well-known places and learning from the registry instead. Most Windows users will not have R on the PATH, so a naked call to R or Rscript is going to fail.

@cscheid thinks this leads to a problem (quarto-dev/quarto#557 (comment)) given

shinylive/_extensions/quarto-ext/shinylive/shinylive.lua

Line 81 in d93c9f2

res = pandoc.pipe("Rscript", args, input)

[kv9898]

Strangely, while rendering from the Quarto CLI works fine for both R and Python, in RStudio I got an error of:

Error running 'shinylive' command. Perhaps you need to install / update the 'shinylive' Python package?

Seems that RStudio executes the filter in a different way than the CLI.

A reprex:

---
title: "Shinylive Python test"
filters:
  - shinylive
---
```{shinylive-python}
#| standalone: true

```

[nshobert]

I wonder if this is similar to an issue I'm having. I'm trying to use Python shinylive extension. I've followed similar steps as you have, though I'm using VSCode and Codespaces.

The Quarto site runs, the shinylive editor renders while the viewer loads, but then the viewer can't load and collapses the whole Shinylive block into a gray line. My Edge browser console says:

Uncaught Error: ServiceWorker controller was not found!
at setupAppProxyPath (shinylive.js:35071:11)

[kv9898]

Hi there. In my case, the site wouldn't run at all, so I guess you are experiencing a separate problem. Your experience sounds like this issue below, maybe checking that one out is useful!

posit-dev/shinylive#133

[nshobert]

kv9898, thank you for the link! Yes, #133 is the issue I'm having. I'm not sure how I missed it when looking in Issues.

Best of luck with your challenge above.

[kv9898]

kv9898, thank you for the link! Yes, #133 is the issue I'm having. I'm not sure how I missed it when looking in Issues.

Best of luck with your challenge above.

You're welcome! There are quite a lot of 'shinylive' repos out there, haha. This repo is for the quarto extension only, while the link I shared with you belongs to the 'main' repo. There are also another 2 'shinylive' repos for the R and Python packages, respectively.

[schloerke]

@cscheid Any suggestions on how to call Rscript properly? Thank you in advance!

[cscheid]

Quarto does this:

https://github.com/quarto-dev/quarto-cli/blob/740829733499855335a7861e3c4f1333a09db45d/src/core/resources.ts#L84-L171

It strikes me that this is such a complicated dance that Quarto should probably make the result of this call available to Lua filters.

[cscheid]

@schloerke

• Resolve Quarto should provide common tool paths to Lua filters quarto-dev/quarto-cli#10999

[cscheid]

The PR is merged, and the quarto.paths.rscript() API entry point will be available starting in Quarto 1.6.23. (Since your extension will probably have to support Quarto 1.5 for a while, you will need to check for the presence of the quarto.paths table.)

[schloerke]

Thank you @cscheid !

[jarbet]

I am having the same issue and error as the OP. When doing quarto preview/render in RStudio on my Windows machine, my shinylive qmd file renders fine without error. However, when trying to render in Positron, I get this error:

Error running 'Rscript' command. Perhaps you need to install / update the 'shinylive' R package?

Interestingly, when I run Sys.which("Rscript") in RStudio, it retruns the correct path. But when I run it in Positron, it returns an empty string.

[kv9898]

I am having the same issue and error as the OP. When doing quarto preview/render in RStudio on my Windows machine, my shinylive qmd file renders fine without error. However, when trying to render in Positron, I get this error:

Error running 'Rscript' command. Perhaps you need to install / update the 'shinylive' R package?

Interestingly, when I run Sys.which("Rscript") in RStudio, it retruns the correct path. But when I run it in Positron, it returns an empty string.

Sounds like R is not on your PATH?

[antoinelucasfra]

Hi all, I am having the same issue as OP, and I opened an issue #76, sorry didn't see this one earlier, but when I'm running from positron it is not detecting Rscript correctly :

> Sys.which("Rscript")
                            Rscript 
"C:\\PROGRA~1\\R\\bin\\Rscript.bat" 

Instead, I would rather detect my actual R version (from rig) : "C:/Program Files/R/R-4.5.1" where I've already added it to the path and it did not change anything

I am on windows, Positron, quarto 1.8.25, R installed with rig