Some packages throw warning upon clean install

[claczny]

Hi,

first of all, thank you for the development of rig.
I am only starting to use it, but I hope that it will turn out to be as helpful as it seems that it can be :)

tl;dr
I installed rig and rstudio following the instructions from https://ivelasq.rbind.io/blog/macos-rig/ on a MacBook Pro M1 Pro with Ventura 13.1.
I did a first install and followed the instructions, i.e., installing via brew and then running rig add release.
I further set up my R development environment according to the instructions with usethis, etc.

However, I ran into the problem that some packages threw a warning that they could not be updated, specifically boot, foreign, Matrix, nlme, and survival, and these packages reside under /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library

My question is now:
What have I been doing wrong or missed?

More details below!
I tried a few things via the RStudio Console, ultimately resorting to rig remove release to go back to a blank slate and see where I screwed up.

cedric.laczny:/Users/cedric.laczny/ $ rig remove release                                                                        [10:13:35]
[INFO] Running `sudo` for removing R versions. This might need your password.
Password:
[WARN] Removing default version, set new default with rig default <version>
[INFO] Removing /Library/Frameworks/R.framework/Versions/4.2-arm64
[INFO] Updating R-* quick links (as needed)

A new rig add release gives me:

$ rig add release                                                                [10:17:08]
[INFO] Running `sudo` for adding new R versions. This might need your password.
Password:
[INFO] arm64-R-4.2.2-arm64.pkg is cached at /tmp/rig/arm64-R-4.2.2-arm64.pkg
[INFO] Running installer
[INFO] > installer: Package name is R 4.2.2 for macOS (ARM64)
[INFO] > installer: Installing at base path /
[INFO] > installer: The install was successful.
[INFO] Forgetting installed versions
[INFO] Fixing permissions
[INFO] Updating R-* quick links (as needed)
[INFO] Adding R-release alias to R 4.2-arm64
[INFO] Setting default CRAN mirror
[INFO] Installing pak for R 4.2-arm64 (if not installed yet)

When I then open Rstudio.app and type update.packages() into the Console, I am getting:

Warning: package 'boot' in library '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library' will not be updated
Warning: package 'foreign' in library '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library' will not be updated
Warning: package 'Matrix' in library '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library' will not be updated
Warning: package 'nlme' in library '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library' will not be updated
Warning: package 'survival' in library '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library' will not be updated

.libPaths() gives me:

[1] "/Users/cedric.laczny/Library/R/arm64/4.2/library"                    
[2] "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library"

and Sys.getenv("R_LIBS_USER") gives me:

[1] "/Users/cedric.laczny/Library/R/arm64/4.2/library"

I then renamed my user-level R library to have this also clean.
Running update.packages() then gives me:

boot :
 Version 1.3-28 installed in /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library 
 Version 1.3-28.1 available at https://cloud.r-project.org
Update? (Yes/no/cancel) y
foreign :
 Version 0.8-83 installed in /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library 
 Version 0.8-84 available at https://cloud.r-project.org
Update? (Yes/no/cancel) Yes
Matrix :
 Version 1.5-1 installed in /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library 
 Version 1.5-3 available at https://cloud.r-project.org
Update? (Yes/no/cancel) Yes
nlme :
 Version 3.1-160 installed in /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library 
 Version 3.1-161 available at https://cloud.r-project.org
Update? (Yes/no/cancel) Yes
survival :
 Version 3.4-0 installed in /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library 
 Version 3.5-0 available at https://cloud.r-project.org
Update? (Yes/no/cancel) Yes
Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  'lib = "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) 

  There is a binary version available but the source version is later:
         binary source needs_compilation
survival  3.4-0  3.5-0              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) 
trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.2/boot_1.3-28.1.tgz'
Content type 'application/x-gzip' length 629022 bytes (614 KB)
==================================================
downloaded 614 KB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.2/foreign_0.8-84.tgz'
Content type 'application/x-gzip' length 339479 bytes (331 KB)
==================================================
downloaded 331 KB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.2/Matrix_1.5-3.tgz'
Content type 'application/x-gzip' length 5249185 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.2/nlme_3.1-161.tgz'
Content type 'application/x-gzip' length 2394611 bytes (2.3 MB)
==================================================
downloaded 2.3 MB


The downloaded binary packages are in
	/var/folders/mv/zv136yrd1_ng4d2w899qj4g0lgzc4c/T//RtmpM5sWqC/downloaded_packages
installing the source package ‘survival’

trying URL 'https://cloud.r-project.org/src/contrib/survival_3.5-0.tar.gz'
Content type 'application/x-gzip' length 6274897 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

* installing *source* package ‘survival’ ...

[...]
installing to /Users/cedric.laczny/Library/R/arm64/4.2/library/00LOCK-survival/00new/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (survival)

The downloaded source packages are in
	‘/private/var/folders/mv/zv136yrd1_ng4d2w899qj4g0lgzc4c/T/RtmpM5sWqC/downloaded_packages’

Calling update.packages() again, gives me, again:

Warning: package 'boot' in library '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library' will not be updated
Warning: package 'foreign' in library '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library' will not be updated
Warning: package 'Matrix' in library '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library' will not be updated
Warning: package 'nlme' in library '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library' will not be updated
Warning: package 'survival' in library '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library' will not be updated

In summary, I am unsure what I have missed/did wrong.
Moreoever, I somehow guess that the five packages here in question do have an update, which is what triggers this warning.
While it is "only" a warning, I'd like to not start a clean install with the knowledge that there will be plenty of warnings going forward 😅
But there are also other packages installed, which I guess would then create "more" problems down the line once they would get updated:

 lh -tr /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
total 0
drwxr-xr-x@ 15 root  admin   480B Jan 10 10:17 utils
drwxr-xr-x@ 11 root  admin   352B Jan 10 10:17 tools
drwxr-xr-x@ 12 root  admin   384B Jan 10 10:17 tcltk
drwxr-xr-x@ 10 root  admin   320B Jan 10 10:17 stats4
drwxr-xr-x@ 11 root  admin   352B Jan 10 10:17 splines
drwxr-xr-x@ 15 root  admin   480B Jan 10 10:17 rpart
drwxr-xr-x@ 12 root  admin   384B Jan 10 10:17 parallel
drwxr-xr-x@ 13 root  admin   416B Jan 10 10:17 nnet
drwxr-xr-x@ 16 root  admin   512B Jan 10 10:17 nlme
drwxr-xr-x@ 11 root  admin   352B Jan 10 10:17 methods
drwxr-xr-x@ 16 root  admin   512B Jan 10 10:17 lattice
drwxr-xr-x@ 15 root  admin   480B Jan 10 10:17 grDevices
drwxr-xr-x@  9 root  admin   288B Jan 10 10:17 datasets
drwxr-xr-x@ 16 root  admin   512B Jan 10 10:17 cluster
drwxr-xr-x@ 14 root  admin   448B Jan 10 10:17 boot
drwxr-xr-x@ 16 root  admin   512B Jan 10 10:17 MASS
drwxr-xr-x@ 22 root  admin   704B Jan 10 10:17 translations
drwxr-xr-x@ 16 root  admin   512B Jan 10 10:17 survival
drwxr-xr-x@ 15 root  admin   480B Jan 10 10:17 stats
drwxr-xr-x@ 16 root  admin   512B Jan 10 10:17 spatial
drwxr-xr-x@ 14 root  admin   448B Jan 10 10:17 mgcv
drwxr-xr-x@ 12 root  admin   384B Jan 10 10:17 grid
drwxr-xr-x@ 11 root  admin   352B Jan 10 10:17 graphics
drwxr-xr-x@ 14 root  admin   448B Jan 10 10:17 foreign
drwxr-xr-x@ 10 root  admin   320B Jan 10 10:17 compiler
drwxr-xr-x@ 10 root  admin   320B Jan 10 10:17 codetools
drwxr-xr-x@ 13 root  admin   416B Jan 10 10:17 class
drwxr-xr-x@ 10 root  admin   320B Jan 10 10:17 base
drwxr-xr-x@ 23 root  admin   736B Jan 10 10:17 Matrix
drwxr-xr-x@ 12 root  admin   384B Jan 10 10:17 KernSmooth

[gaborcsardi]

This is because rig creates a user package library (see FAQ in the README), and makes the system library read-only for regular users. I guess you get the warning because you can't update packages in a read only library. But that is fine, you can install newer versions of these packages into the user library, and pak does this automatically:

❯ pak::pkg_status("boot")[, c("library", "package", "version")]
# A data frame: 2 × 3
  library                                                              package version
* <chr>                                                                <chr>   <chr>
1 /Users/gaborcsardi/Library/R/arm64/4.2/library                       boot    1.3-28.1
2 /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library boot    1.3-28

If you really want to update packages in the system library, start R as the root user, and call

update.packages(lib.loc = .Library)

[claczny]

Thank you. I seem to recall that this is what I did in the past, but it still complained about the older system libraries, which was puzzling to me.
So basically, having the same library but in different versions ...
Will check this again and let you know.