quarto: unable to locate R installation

General
1

I am using Mac OS Monterey Version 12.4. When attempting to render Quarto, I see the following error:

Error in assignInNamespace("htmlPreserve", htmlPreserve, ns = "htmltools") : 
  could not find function "assignInNamespace"
Calls: .main -> source -> withVisible -> eval -> eval
Execution halted
Error in packageVersion("rmarkdown") : 
  could not find function "packageVersion"
Calls: cat -> paste0
Execution halted

Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/

What I have done so far to try to address this issue:

  1. Downloaded the latest versions of R (4.2.1), R Studio (2022/07, 1-554), and Quarto (1.0.38), and the rmarkdown package (2.14) [FYI, I just checked rmarkdown's package version with packageVersion - which the error claims is not loaded]
  2. Tried to manually set the PATH to the R library(s): Adding to the PATH variable
old_path <- Sys.getenv("PATH")

Sys.setenv(PATH = paste(old_path, "/Library/Frameworks/R.framework/Resources/library", sep = ":"))

I suspect the issue is because I am working in a project located on a Box (i.e. in the cloud) directory. I am able to use R just fine in R Studio, so it must be a Quarto specific issue with accessing R when working in a cloud environment(?).

Any assistance is greatly appreciated!

1 Like
2

Are you working inside or outside RStudio IDE ?

Can you share the result of quarto check please ?
This should tell us what Quarto is seeing - like finding R installation or not.

Thank you !

3

My apologies! Inside R Studio IDE.

Here is quarto check


Elizabeths-MacBook-Pro:r elizabethdavis$ quarto check

[✓] Checking Quarto installation......OK
      Version: 1.0.38
      Path: /Applications/quarto/bin

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

[✓] Checking Python 3 installation....OK
      Version: 3.8.9
      Path: /Library/Developer/CommandLineTools/usr/bin/python3
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

(|) Checking R installation...........Error in packageVersion("rmarkdown") : 
  could not find function "packageVersion"
Calls: cat -> paste0
Execution halted
[✓] Checking R installation...........(None)

      Unable to locate an installed version of R.
      Install R from https://cloud.r-project.org/
4

Can you try our latest version ?

Just to see if the problem is fixed there ?

Thank you.

5

also this message can happen when R does not load the default packages by default, among which utils.

Usually this happens if you have options(defaultPackages = character()) or R_DEFAULT_PACKAGES=NULL set somewhere in your environment.

Example with Powershell

> $env:R_DEFAULT_PACKAGES=$null
> Rscript --vanilla -e "packageVersion('rmarkdown')"
[1] '2.16.1'

> $env:R_DEFAULT_PACKAGES="NULL"
> Rscript --vanilla -e "packageVersion('rmarkdown')"
Erreur dans packageVersion("rmarkdown") :
  impossible de trouver la fonction "packageVersion"
ExĂ©cution arrĂȘtĂ©e

We'll improve that on our side, but still a specific use case.

Do you have one of those configuration set by any chance ?

I have added an issue for this anyway: Correctly namespace usage of R default package functions like utils · Issue #2187 · quarto-dev/quarto-cli · GitHub

6

Thank you very much Christophe. I have downloaded the latest Quarto version, but I am still encountering the same issue. I don't believe I have either of the options you suggested set;

From the digging I have done, it looks like one possibility is that the error is to do with my PATH. However, when I have tried to manually set the PATH, it has not fixed the problem.

Thank you for looking into this!

7

Hi,

I edited your post to hide the env var. Lost of personal info from your system not needed.

I saw /Users/elizabethdavis/Applications/quarto/binso it seems that Quarto is indeed in your path.

but I am still encountering the same issue.

The issue with packageVersion not found ?

This is thrown by Quarto, so it means it is found in PATH. But somehow, utils package is not used in your R installation.

Can you check that it work on your R installation :

utils::packageVersion("rmarkdown")
8

Hi,
Thank you! The output of utils::packageVersion("rmarkdown") is '2.14'.

And yes, same errors as before when I attempt to render the hello.qmd doc:

Error in assignInNamespace("htmlPreserve", htmlPreserve, ns = "htmltools") : 
  could not find function "assignInNamespace"
Calls: .main -> source -> withVisible -> eval -> eval
Execution halted
Error in packageVersion("rmarkdown") : 
  could not find function "packageVersion"
Calls: cat -> paste0
Execution halted

Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/

I have redownloaded R a few times now to try to address this issue, and have not changed the download path. I wonder if it is something to do with administrative privileges on my machine, although as far as I know I have sole control over it- there are no other user accounts.

Thank you very much again for all of your assistance with this.

9

This should be fixed in future version of Quarto

However, you should be able to make it work by checking what I shared before

R utils package should be installed and loaded in R by default. I don't know what is the issue.

10

Thank you Christophe. I tried what you suggested, but it seemed like Quarto was still unable to locate my installation of R. I am really not sure how to fix the problem, but have "solved" it by rendering the documents using R Studio Cloud. I will test the IDE again after the next release of Quarto, to see if your fix has solved the problem.

Thank you for all of your assistance with this!

1 Like
11

Ok great.

You could already try the pre-release of Quarto to see if this is fixed:

12

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