Packages not update on Mac

[jynusmac]

Rstudio Versión 2023.06.2+561 (2023.06.2+561) on a Mac mini (2018) with MacOs Monterey 12.6.7
On packages pane click on update gives me a list of packages to update:

I select all, run install updates and all seems go well:

And when I click again in packages pane for updates, all are there again:

Any idea on what is wrong?

[Gabor]

Maybe the package versions are cached. Did you try restarting R and/or RStudio?

If yes, then can you please include the full output of the installation?

[jynusmac]

I have just restarted R and Rstudio. This is what appears in the console.

> 

Restarting R session...

> install.packages(c("classInt", "credentials", "DescTools", "deSolve", "geojsonio", "ggfittext", "googlePolylines", "mapsf", "pbdZMQ", "rgl", "terra"))
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/classInt_0.4-9.tgz'
Content type 'application/x-gzip' length 499138 bytes (487 KB)
==================================================
downloaded 487 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/credentials_1.3.2.tgz'
Content type 'application/x-gzip' length 170633 bytes (166 KB)
==================================================
downloaded 166 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/DescTools_0.99.49.tgz'
Content type 'application/x-gzip' length 6062373 bytes (5.8 MB)
==================================================
downloaded 5.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/deSolve_1.37.tgz'
Content type 'application/x-gzip' length 2685428 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/geojsonio_0.11.2.tgz'
Content type 'application/x-gzip' length 986377 bytes (963 KB)
==================================================
downloaded 963 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/ggfittext_0.10.0.tgz'
Content type 'application/x-gzip' length 829148 bytes (809 KB)
==================================================
downloaded 809 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/googlePolylines_0.8.3.tgz'
Content type 'application/x-gzip' length 1223878 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/mapsf_0.7.0.tgz'
Content type 'application/x-gzip' length 2226765 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/pbdZMQ_0.3-9.tgz'
Content type 'application/x-gzip' length 824323 bytes (805 KB)
==================================================
downloaded 805 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/rgl_1.1.3.tgz'
Content type 'application/x-gzip' length 10635600 bytes (10.1 MB)
==================================================
downloaded 10.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/terra_1.7-39.tgz'
Content type 'application/x-gzip' length 101461332 bytes (96.8 MB)
==================================================
downloaded 96.8 MB


The downloaded binary packages are in
	/var/folders/h3/gbg9fh2x6kvgrpzw8tpbj5qh0000gn/T//RtmpVKhzCX/downloaded_packages

Packages are not updated by the way

[Gabor]

Yeah, the installation output should start with:

❯ install.packages(c("classInt", "credentials"))
Installing packages into ‘/Users/gaborcsardi/Library/R/arm64/4.3/library’
(as ‘lib’ is unspecified)

but I assumed that RStudio just left that out for some reason....

It is possible, that you are installing these packages into a different library, than the one you are using in the current RStudio project? E.g. check the output of

.libPaths()

to see the libraries.

In any case a workaround is to copy-paste that install.packages() command into the console and run it from there. Not very elegant, I agree.

[jynusmac]

This is the output:

> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library"

Using install.packages(c("classInt", "credentials", "DescTools", "deSolve", "geojsonio", "ggfittext", "googlePolylines", "mapsf", "pbdZMQ", "rgl", "terra")) gave the same result...

[Gabor]

Oh, wait, this is because CRAN does not have binary packages available for these packages. E.g.: CRAN - Package classInt shows

Version:	0.4-10
[...]
macOS binaries:	r-release (arm64): classInt_0.4-9.tgz, r-oldrel (arm64): classInt_0.4-9.tgz, r-release (x86_64): classInt_0.4-9.tgz, r-oldrel (x86_64): classInt_0.4-10.tgz

So RStudio is right, there is a newer packages available, just not in the macOS binary form, which is the default package type used by install.packages(). If you really want to update them, add type = "source" to the install.packages() call, but note that you might run into installation errors if you are installing packages from source.

[jynusmac]

Thanks Gabor, I'll wait for mac packages available then.

Regards.

[coforfe]

Thanks!.

What I see is that the parameter to include in "install.packages()" is "type", right?.

Thanks again,
Carlos.

[Gabor]

Right, sorry. The corresponding option is called pkgType, the argument is type. I'll fix it in my answer.