Can't render quarto doc with specific packages in vscode, but in RStudio

[werkstattcodes]

Hello,

I am encountering a strange behavior when using Quarto in vscode. When my script includes the packages writexl, summarytools or treemapify, I can't render the document. I can run the chunks without problem, but i can't render the document to html. vscode/quarto tells me that the package doesn't exist.

Oddly, when I open the same file in RStudio, I can render the document without problem.

I already filed an issue in quarto/vscode rep, but maybe someone here encountered the issue as well and has already a remedy.

Many thanks.

---

title: "test_vscode_writexl"
format: html

library(writexl)
library(summarytools)
library(treemapify)

Error in library(writexl) : there is no package called 'writexl'
Calls: .main ... withCallingHandlers -> withVisible -> eval -> eval -> library

[cderv]

When you are in vscode,

• does this happen also with R Markdown document the same issue ?
• if you open a R terminal in VS code, can you load the writexl package ?
• Can you compare .libPaths() result from R console in R Studio and R terminal in VScode ?
• Can you share results of quarto check from VSCODE terminal ?

[werkstattcodes]

Many thanks for your reply. Below my answers.

does this happen also with R Markdown document the same issue ?

I am encountering an issue when trying to render rmarkdown docs in vscode.

in vscode

library(rmarkdown)
pandoc_available()
[1] FALSE

in RStudio

> library(rmarkdown)
> pandoc_version()
[1] ‘2.18’

if you open a R terminal in VS code, can you load the writexl package ?
Yes

Can you compare .libPaths() result from R console in R Studio and R terminal in VScode ?
VScode
C:/Program Files/R/R-4.2.0/library"

RStudio

[1] "C:/Users/Roland/AppData/Local/R/win-library/4.2"
[2] "C:/Program Files/R/R-4.2.0/library" 

Can you share results of quarto check from VSCODE terminal ?
Sorry, think i don't understand. What do you mean with "quarto check".

It seems there might be an issue with my .libPaths. But it's strange that i can call the packages interactively (comandline, chunks).

I added the "C:/Users/Roland/AppData/Local/R/win-library/4.2" under the vscode r extension setting R:lib paths.

VSCode .libPaths() reads now as below, but the issue remains. I can't render the quarto document.

> .libPaths()
[1] "C:/Users/Roland/AppData/Local/R/win-library/4.2"
[2] "C:/Program Files/R/R-4.2.0/library"

[cderv]

Yes it seems the .libPaths() is not correctly loaded I wonder if quarto finds the same R version when rendering. I believe when running interactively, the R version set up in R extension in VSCODE is used.

Are you using rig for R installation ?

Sorry, think i don't understand. What do you mean with "quarto check".

Open a terminal window in VS code and type quarto check

Also, you could try rendering the document outside for VSCODE in Terminal. It depends how you set up quarto also.

quarto check should help us I believe.

[werkstattcodes]

Thanks again.
If I am reading the results correctly, you were right. Quarto is using R 4.0.3, not R 4.2. Any idea how I can change this?

[>] Checking Quarto installation......OK
      Version: 1.0.16
      Path: C:\Users\Roland\AppData\Local\Programs\Quarto\bin\
      CodePage: 1252

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

[>] Checking Python 3 installation....OK
      Version: 3.10.5
      Path: C:/Users/Roland/AppData/Local/Programs/Python/Python310/python.exe
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with py -m pip install jupyter

[>] Checking R installation...........OK
      Version: 4.0.3
      Path: C:/PROGRA~1/R/R-40~1.3
      LibPaths:
        - C:/Users/Roland/Documents/R/win-library/4.0
        - C:/Program Files/R/R-4.0.3/library
      rmarkdown: 2.11

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

[cderv]

Do you have a R version set in your PATH ? Can you check that ?
You can open variable environement windows on Windows on in powershell window type

$env:PATH -split ";"

It seems you have several R version installed, so you can also remove 4.0.3 if you don't use it anymore. That should solve the issue.

[werkstattcodes]

Deleted the older R versions. Issue solved. Many thanks (as so often)! This was very helpful.

[cderv]

For reference, issue related to this question: quarto-dev/quarto-vscode#38