Cannot install packages on R 4.4.1 or .2 on Sequoia

General
1

I just updated my MacBook Pro (Intel x86) to Sequoia 15.2. Also, I updated to the most recent version of R Studio (2024.12.0+467) and CRAN R 4.4.2. When I try to install packages using the standard install.packages command, (for example, install.packages("devtools")) it fails on multiple steps saying "permission denied" to the appropriate framework folder. Here's an example of the warning:

  cannot open compressed file '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/askpass/DESCRIPTION', probable reason 'Permission denied'

I am a full administrator on my computer, so I'm not sure why I wouldn't have rw permissions to the appropriate folders, like I did before upgrading. See screenshot below:
Screenshot 2024-12-29 at 1.26.14 PM
Is this something with the new Mac OS Sequoia (I'm suspicious it is)? Or is it something with the new R Studio? I also "downgraded" to my last version of R 4.4.1, and had the same issue. I tried installing packages via the R Studio GUI - same issue. Any ideas? Thanks,

2

Even if you are an administrator, you are probably not running R with administrator privileges. So you would have to make the system library writeable for everyone if you want to install packages there.

I suggest you don't do that, but rather create a package library for your user:

dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)

Then restart R, so the new library is picked up, and install packages there.

You might also find our rig [1] tool useful , it will create a user library for you automatically and it also helps you switch between R versions.

[1] GitHub - r-lib/rig: The R Installation Manager

3

This didn't work. I created the new directory as above, restarted R and R studio, and tried to load a known package; failed because the new directory didn't have any packages in it. Then, I copied all my packages from my legacy framework location to the new user library directory. After which, I changed my Rprofile file to direct to the new directory for .libPaths. I tried to load packages, and it errors, as it still seems to reference the original location for some /Meta files. I really feel like this is some sort of issue with some strange new security built into Mac OS Sequoia. I'm going to uninstall everything, and start over with a clean install and see if that works.

4

Okay, so went with clean install, and did what you suggested and it worked. I also changed my .Rprofile file to have the user directory be my first and default as well (I don't know if that's necessary or not). I also downloaded rig and will try that out. The biggest problem I have is maintaining my libraries and install versions across several computers - I hope that rig can help with that. Thanks for your help on this.

5

It is not necessary. The user library is picked up automatically, so it is best not to change the library path at all in your .Rprofile, especially because the profile is not loaded in --vanilla sessions.