Error In Desc$Repository : $ Operator Is Invalid For Atomic Vectors

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Bug Description

When running quarto render on a qmd file with shinylive chunk, you may encounter an error that reads "Error in desc$Repository : $ operator is invalid for atomic vectors." This error typically occurs when the shinylive chunk installs webR packages, such as webr::install("ggplot2"). This issue is particularly frustrating when you've previously used the same quarto document without any issues, only to encounter this error upon revisiting it after a few months.

Steps to Reproduce

To reproduce this error, follow these steps:

  1. Create a directory with the following structure:

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

2. Create an `index.qmd` file with the following content:
   ```markdown
---
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)
  1. Run quarto render index.qmd to reproduce the error.

Your Environment

To troubleshoot this issue, it's essential to understand your environment. Here are the details of your system:

  • System Version: macOS 15.4 (24E248)
  • Kernel Version: Darwin 24.4.0
  • R version: 4.4.1* quarto version: 1.6.42
  • shinylive version: 0.3.0.9000

Quarto Check Output

The quarto check output is as follows:

[✓] 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

Troubleshooting

To troubleshoot this issue, you can try the following:

  1. Update the shinylive package: Ensure that the shinylive package is up-to-date by running install.packages("shinylive").
  2. Check the quarto version: Verify that you're using the latest version of quarto by running quarto --version.
  3. Check the R version: Ensure that you're using the latest version of R by running R --version.
  4. Check the R environment: Verify that the R environment is properly set up by running Rscript -e "sessionInfo()".
  5. Check the quarto cache: Clear the quarto cache by running quarto cache clear and then try rendering the document again.

If none of these troubleshooting steps resolve the issue, you may want to consider seeking further assistance from the quarto community or the shinylive package maintainers.

Q: What is the error "Error in desc$Repository : $ operator is invalid for atomic vectors" and how can I fix it?

A: The error "Error in desc$Repository : $ operator is invalid for atomic vectors" typically occurs when the shinylive chunk installs webR packages, such as webr::install("ggplot2"). This error can be frustrating, especially when you've previously used the same quarto document without any issues. To fix this error, try updating the shinylive package by running install.packages("shinylive").

Q: What are the system requirements for quarto and shinylive?

A: The system requirements for quarto and shinylive are as follows:

  • System Version: macOS 15.4 (24E248)
  • Kernel Version: Darwin 24.4.0
  • R version: 4.4.1
  • quarto version: 1.6.42
  • shinylive version: 0.3.0.9000

Q: How can I troubleshoot the error "Error in desc$Repository : $ operator is invalid for atomic vectors"?

A: To troubleshoot this error, you can try the following:

  1. Update the shinylive package: Ensure that the shinylive package is up-to-date by running install.packages("shinylive").
  2. Check the quarto version: Verify that you're using the latest version of quarto by running quarto --version.
  3. Check the R version: Ensure that you're using the latest version of R by running R --version.
  4. Check the R environment: Verify that the R environment is properly set up by running Rscript -e "sessionInfo()".
  5. Check the quarto cache: Clear the quarto cache by running quarto cache clear and then try rendering the document again.

Q: What are the common causes of the error "Error in desc$Repository : $ operator is invalid for atomic vectors"?

A: The common causes of this error are:

  • Outdated shinylive package
  • Outdated quarto version
  • Outdated R version
  • Incorrect R environment setup
  • Quarto cache issues

Q: How can I prevent the error "Error in desc$Repository : $ operator is invalid for atomic vectors" from occurring in the future?

A: To prevent this error from occurring in the future, you can try the following:

  1. Regularly update the shinylive package: Ensure that the shinylive package is up-to-date by running install.packages("shinylive").
  2. Regularly update the quarto version: Verify that you're using the latest version of quarto by running quarto --version.
  3. Regularly update the R version: Ensure that you're using the latest version of R by running R --version.
  4. Verify the R environment setup: Ensure that the R environment is properly set up by running Rscript -e "sessionInfo()".
  5. Clear the quarto cache regularly: Clear the quarto cache by running quarto cache clear to prevent cache-related issues.

Q: Where can I find more information about the error "Error in desc$Repository $ operator is invalid for atomic vectors"?

A: For more information about this error, you can try the following:

  1. Check the quarto documentation: Visit the quarto documentation website for more information about the error and its causes.
  2. Check the shinylive documentation: Visit the shinylive documentation website for more information about the error and its causes.
  3. Check the R documentation: Visit the R documentation website for more information about the error and its causes.
  4. Check online forums and communities: Visit online forums and communities, such as the quarto community or the shinylive community, for more information about the error and its causes.