Error in desc$Repository : $ operator is invalid for atomic vectors

[royfrancis]

Bug description

I get this error when running quarto render on a qmd file with shinylive chunk. This is a quarto document that used to work. Now coming back it after a year and running with newer version of tools, it gives this error.

When I run quarto render index.qmd

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/ragg_1.3.3.tgz'
Content type 'application/x-tar' length 692282 bytes (676 KB)
==================================================
downloaded 676 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/rbibutils_2.3.tgz'
Content type 'application/x-tar' length 1056089 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

Error in desc$Repository : $ operator is invalid for atomic vectors
Calls: <Anonymous> ... download_wasm_packages -> lapply -> FUN -> prepare_wasm_metadata
In addition: There were 12 warnings (use warnings() to see them)
Execution halted
(E) Error running 'Rscript' command. Perhaps you need to install / update the 'shinylive' R package?
 Error:
 pandoc.pipe.error {command: "Rscript", error_code: 1, output: ""}
Error running filter /Applications/quarto/share/filters/main.lua:
...shinylive/_extensions/quarto-ext/shinylive/shinylive.lua:40: Error running 'Rscript' command. Perhaps you need to install / update the 'shinylive' R package?

stack traceback:
	...shinylive/_extensions/quarto-ext/shinylive/shinylive.lua:40: in global 'throw_quarto_error'
	...shinylive/_extensions/quarto-ext/shinylive/shinylive.lua:86: in global 'callRShinylive'
	...shinylive/_extensions/quarto-ext/shinylive/shinylive.lua:113: in global 'callShinylive'
	...shinylive/_extensions/quarto-ext/shinylive/shinylive.lua:437: in function <...shinylive/_extensions/quarto-ext/shinylive/shinylive.lua:408>
	[C]: in ?
	[C]: in method 'walk'
	/Applications/quarto/share/filters/main.lua:558: in local 'checked_walk'
	/Applications/quarto/share/filters/main.lua:610: in function 'run_emulated_filter'
	/Applications/quarto/share/filters/main.lua:1297: in local 'callback'
	[string "..."]:1888: in field 'withScriptFile'
	/Applications/quarto/share/filters/main.lua:1313: in upvalue 'run_emulated_filter_chain'
	/Applications/quarto/share/filters/main.lua:1351: in function </Applications/quarto/share/filters/main.lua:1348>
stack traceback:
	/Applications/quarto/share/filters/main.lua:558: in local 'checked_walk'
	/Applications/quarto/share/filters/main.lua:610: in function 'run_emulated_filter'
	/Applications/quarto/share/filters/main.lua:1297: in local 'callback'
	[string "..."]:1888: in field 'withScriptFile'
	/Applications/quarto/share/filters/main.lua:1313: in upvalue 'run_emulated_filter_chain'
	/Applications/quarto/share/filters/main.lua:1351: in function </Applications/quarto/share/filters/main.lua:1348>

I am not really sure if the issue is shinylive quarto extension, shinylive, shinylive R package or something else altogether. Since quarto and the extension is my entry point, I decided to report it here.

Steps to reproduce

This is my directory setup:

.
|-- _extensions
|   `-- quarto-ext
|       `-- shinylive
`-- index.qmd

Here is the index.qmd file:

---
title: "Shinylive"
format: html
filters:
  - shinylive
---

```{shinylive-r}
#| standalone: true
#| viewerHeight: 450

webr::install(c("ggplot2", "bslib", "palmerpenguins", "htmltools"))

library(htmltools)
library(bslib)
library(ggplot2)
library(palmerpenguins)
data("penguins")

pdata <- na.omit(penguins)
pc <- prcomp(pdata[,c("bill_length_mm", "bill_depth_mm", "flipper_length_mm", "body_mass_g")], center = TRUE, scale. = TRUE)
dfr <- cbind(pdata,as.data.frame(pc$x))

ui <- page_sidebar(
  sidebar = sidebar(
    selectInput("x",
      label = "X axis",
      choices = c("PC1","PC2","PC3","PC4"),
      selected = "PC1"
    ),

    selectInput("y",
      label = "Y axis",
      choices = c("PC1","PC2","PC3","PC4"),
      selected = "PC2"
    ),
    selectInput("v",
      label = "Color",
      choices = c("species", "island", "sex"),
      selected = "cut"
    )
  ),
  imageOutput("plot", height = "350px")
)

server <- function(input, output, session) {

  output$plot <- renderImage({
    x <- input$x
    y <- input$y
    v <- input$v

    p <- ggplot(dfr, aes(x = !!sym(x), y = !!sym(y), col = !!sym(v))) +
      geom_point() +
      theme_bw() +
      theme(legend.position = "top")

    file <- htmltools::capturePlot(
      print(p),
      tempfile(fileext = ".svg"),
      grDevices::svg,
      width = 4,
      height = 4
    )

    list(src = file)
  }, deleteFile = TRUE)
}

app <- shinyApp(ui = ui, server = server)
```

Your environment

System Version: macOS 15.4 (24E248)
Kernel Version: Darwin 24.4.0

$ quarto list extensions
Id                      Version    Contributes
quarto-ext/shinylive    0.2.0      filters

$ Rscript -e "packageVersion('shinylive')"
[1] '0.3.0.9000'

$ Rscript -e "sessionInfo()"
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin13.4.0
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/liblapack-netlib.3.9.0.dylib

locale:
[1] C

time zone: Europe/Stockholm
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.4.1

The versions mentioned above are when running in a conda environment on Mac. I have also tried this in an ubuntu docker container and get the same error.

Quarto check output

Quarto 1.6.42
[✓] Checking environment information...
Quarto cache location: /Users/royfr474/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.4.0: OK
Dart Sass version 1.70.0: OK
Deno version 1.46.3: OK
Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.6.42
Path: /Applications/quarto/bin

[✓] Checking tools....................OK
TinyTeX: (external install)
Chromium: (not installed)

[✓] Checking LaTeX....................OK
Using: TinyTex
Path: /Users/royfr474/Library/TinyTeX/bin/universal-darwin
Version: 2024

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
Version: 3.9.18 (Conda)
Path: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/bin/python
Jupyter: 5.7.1
Kernels: python3

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
Version: 4.4.1
Path: /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R
LibPaths:
- /opt/homebrew/Caskroom/miniforge/base/envs/r-4.4/lib/R/library
knitr: 1.49
rmarkdown: 2.29

[✓] Checking Knitr engine render......OK

[royfrancis]

I went back to old docker container from a year ago and tried on the same qmd and it works. So I assume it's something to do with the newer version. The old versions that worked together were

quarto 1.4.549
shinylive-0.2.3
shinylive quarto extension 0.1.0
shinylive r version 0.1.1

[wch]

It looks like this is coming from the R shinylive package, and I just file an issue there: posit-dev/r-shinylive#150

[wch]

I am not able to reproduce this problem when I follow your exact instructions. One possibly significant difference is that I am not using Conda.

I also noticed that your log shows it downloading ragg and rbibutils. Mine doesn't try to download those.

Click to see output

❯ quarto render index.qmd      
pandoc 
  to: html
  output-file: index.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
  
ℹ Loading metadata database
✔ Loading metadata database ... done

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/ggplot2_3.5.1.tgz'
Content type 'application/x-tar' length 4196030 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/colorspace_2.1-1.tgz'
Content type 'application/x-tar' length 2425563 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/fansi_1.0.6.tgz'
Content type 'application/x-tar' length 252633 bytes (246 KB)
==================================================
downloaded 246 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/farver_2.1.2.tgz'
Content type 'application/x-tar' length 1311148 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/gtable_0.3.6.tgz'
Content type 'application/x-tar' length 177854 bytes (173 KB)
==================================================
downloaded 173 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/isoband_0.2.7.tgz'
Content type 'application/x-tar' length 1611696 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/labeling_0.4.3.tgz'
Content type 'application/x-tar' length 40461 bytes (39 KB)
==================================================
downloaded 39 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/lattice_0.22-6.tgz'
Content type 'application/x-tar' length 927645 bytes (905 KB)
==================================================
downloaded 905 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/MASS_7.3-65.tgz'
Content type 'application/x-tar' length 851719 bytes (831 KB)
==================================================
downloaded 831 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/Matrix_1.7-3.tgz'
Content type 'application/x-tar' length 2858416 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/mgcv_1.9-1.tgz'
Content type 'application/x-tar' length 1561876 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/munsell_0.5.1.tgz'
Content type 'application/x-tar' length 223023 bytes (217 KB)
==================================================
downloaded 217 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/nlme_3.1-167.tgz'
Content type 'application/x-tar' length 1701826 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/pillar_1.10.1.tgz'
Content type 'application/x-tar' length 486641 bytes (475 KB)
==================================================
downloaded 475 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/pkgconfig_2.0.3.tgz'
Content type 'application/x-tar' length 16485 bytes (16 KB)
==================================================
downloaded 16 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/RColorBrewer_1.1-3.tgz'
Content type 'application/x-tar' length 25384 bytes (24 KB)
==================================================
downloaded 24 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/scales_1.3.0.tgz'
Content type 'application/x-tar' length 512986 bytes (500 KB)
==================================================
downloaded 500 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/tibble_3.2.1.tgz'
Content type 'application/x-tar' length 557365 bytes (544 KB)
==================================================
downloaded 544 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/utf8_1.2.4.tgz'
Content type 'application/x-tar' length 111761 bytes (109 KB)
==================================================
downloaded 109 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/vctrs_0.6.5.tgz'
Content type 'application/x-tar' length 928374 bytes (906 KB)
==================================================
downloaded 906 KB

trying URL 'http://repo.r-wasm.org/bin/emscripten/contrib/4.4/viridisLite_0.4.2.tgz'
Content type 'application/x-tar' length 1293388 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

Warning messages:
1: In find.package(pkgs, lib.loc = NULL, quiet = FALSE, !is_quiet()) :
  there is no package called ‘palmerpenguins’
2: In find.package(pkgs, lib.loc = NULL, quiet = FALSE, !is_quiet()) :
  there is no package called ‘webr’
Output created: index.html

Here's some info for my system:

❯ quarto list extensions
Id                      Version    Contributes
quarto-ext/shinylive    0.2.0      filters    

❯ Rscript -e "packageVersion('shinylive')"
[1] ‘0.3.0.9000’

❯ Rscript -e "sessionInfo()"
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.3.2

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.4.2