[R-SIG-Mac] update.packages() cannot install from source

[Spencer Graves]

Hello, All:


       "update.packages()" fails for me on packages DescTools, digest, 
jpeg, mgcv, openxlsx, rlang, and spam.  It first says:


   There are binary versions available but the
   source versions are later:
            binary  source needs_compilation
DescTools 0.99.29 0.99.30              TRUE
digest     0.6.21  0.6.22              TRUE
jpeg        0.1-8 0.1-8.1              TRUE
mgcv       1.8-29  1.8-30              TRUE
openxlsx  4.1.0.1   4.1.2              TRUE
rlang       0.4.0   0.4.1              TRUE
spam        2.3-0 2.3-0.2              TRUE


       It then asks, "Do you want to install from sources the packages 
which need compilation? (Yes/no/cancel)".  I reply "y" or "Yes".  For 
each package, it says it was

... successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘DescTools’
* removing 
‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/DescTools’
* restoring previous 
‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/DescTools’


       A web search for "xcrun: error: invalid active developer path" 
identified a couple of discussions on StackExchange that say that I need 
to have Xcode installed correctly.  I think I have everything up to 
date:  macOS 10.15.1 Catalina with Xcode downloaded and installed via 
the App store.  RStudio 1.2.5001 with:


sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.1

Matrix products: default
BLAS: 
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets
[6] methods   base

loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1


"https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a" 
recommends, "xcode-select --install", which to me seems like it should 
be equivalent to the install I just did via the App Store. This 
StackExchange discussion also said, "If the above alone doesn't do it, 
then also run:  xcode-select --reset".  However, before I do that, I 
thought I'd ask here if anyone else is having a problem like this.  And 
if yes, and if they've fixed it, what did they do to fix it?


       Thanks,
       Spencer Graves