Updating packages fails with error message: “Updating loaded packages”

[francisbarton]

I am getting an error when I try to update my R packages (via the Packages pane > Update but I don't think this matters). I haven't had this error before - it seems to have just invented itself recently to make my life difficult I could update fine just a couple of days ago.

There's no real error message to help me work out what the issue is. This is what I see in the console:

> install.packages(c("blogdown", "bookdown", "geometry", "hms", "lpSolve", "pkgbuild", "rgl", "RgoogleMaps", "rmarkdown", "sys", "whisker", "zip"))
Error in install.packages : Updating loaded packages

[comes up with dialogue about restarting R to allow update]

Restarting R session...

> install.packages(c("blogdown", "bookdown", "geometry", "hms", "lpSolve", "pkgbuild", "rgl", "RgoogleMaps", "rmarkdown", "sys", "whisker", "zip"))

Restarting R session...

Error: Unable to establish connection with R session

I'm using RStudio, and have R 3.6.1 on 64-bit Windows 10.

I've done a Windows reboot and it's the same issue after doing that.

Any ideas please?

[mara]

Does it work for you in R, but not in RStudio? (see FAQ below for disambiguation)

Differentiating R from RStudio

Aside: goals for this thread

I'm hoping this will help people disambiguate R from RStudio, and also help with getting questions in the right category. This is a bit of a mashup of the times I've tried to explain this in individual threads, so please feel free to add to this topic for further clarification/point out corrections, etc.

Before putting a code-related question in the #rstudio-ide category or using the rstudio tag, it's helpful to ask yourself: Does this work in the regular R GUI, but not when you're in RStudio? If you're using RStudio, you're using R — RStudio is just an IDE (Integrated Development Environment) in which you are using the R language. (On of my favourite fi…

[francisbarton]

Thanks Mara.
I just opened up the RGui itself and pasted the install.packages line at the prompt and it worked smooth as you like. Weird.
So I'm not sure what the problem is with R within RStudio, maybe there's something affecting the R setup within the IDE that isn't to do with R itself. As I say, I have not had this problem before, it's suddenly started.

[mara]

Very strange. I'm going to move this to the IDE category, and they can help you troubleshoot from there.

[kevinushey]

The most likely culprit is that you are loading the packages that you're trying to reinstall in e.g. your .Rprofile, or you have R objects in your workspace that are forcing these packages to be reinstalled. See also:

IDE keeps getting stuck in a loop to restart R when trying to install a package that is already installed