Error: could not find function "update.packages" on start up, and cannot render in knitr

[Ian_T]

Upon start up in R studio, the R console shows:

Error: could not find function "update.packages"

I attempted to render a document with R markdown, though an error message was returned:

Error: could not find function "update.packages"

Not sure that a discrepancy in the file paths using find.package("utils") and path.package("utils") is a contributing factor/issue

Any help is greatly appreciated.

R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
R studio (2023.09.1 Build 494)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[jrkrideau]

I do not think you can update packages in an Rmd document /environment.

If you want to update packages you should do it in the General Environment, that is the one that loads automatically when you start RStudio normally.

[Gabor]

You mean you did not run that function yourself? Do you have update.packages() in your .Rprofile file?

[Ian_T]

The update .packages() command comes up during start up, I didn't put it in the Rmd document, when pressing the knit but the render tab opens and shows the error message.

R on start up

Render tab after pressing knit

[Ian_T]

I did not run that function, that is what shows on start up. update.packages() is not in my .Rprofile file.

[Gabor]

Sorry, I meant your user's profile, not the system profile, i.e. what is the output of this?

writeLines(readLines("~/.Rprofile"))

Make sure that you omit sensitive information!

Also, please copy and paste the output between markdown fences, i.e. three ``` characters, like this :

```
<your output>
```

[Ian_T]

The output I received are:

writeLines(readLines("~/.Rprofile"))
update.packages(ask = FALSE)

[Gabor]

Yes, so you do have update.packages() in your profile. Remove that line from ~/.Rprofile.

[Ian_T]

That worked! thanks so much I have some research to do on what .RProfile is and why it is important.

[Gabor]

Every time an R process starts up, it runs the code from your .Rprofile. See

?.Rprofile