[R-SIG-Mac] Link to headers lost? Headers not where they should be?

[Bryan Hanson]

I don’t know how/when this problem arose, but as of a few days ago, I can’t build source packages any longer.  I’ve been through quite a lot of resources looking for answers and no luck so far, so turning to the mercies of this list.

I have this problem with either R 4.1.1 or R 4.2.0  I’ve disabled .Rprofile and .cshrc files and the problem persists.  Running BigSur 10.16

When I try for instance to install MASS (as an example, the problem occurs with any pkg needing compilation) I see this:

[Abbott-2:~/Desktop] bryanhanson% R CMD INSTALL MASS
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘MASS’ ...
** package ‘MASS’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/usr/local/clang4/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c MASS.c -o MASS.o
MASS.c:18:10: fatal error: 'stdlib.h' file not found
#include <stdlib.h>
         ^~~~~~~~~~
1 error generated.
make: *** [MASS.o] Error 1
ERROR: compilation failed for package ‘MASS’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/MASS’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/MASS’

I think this feedback says the compiler is present and working. 

Most resources about "fatal error: 'stdlib.h' file not found” end up being cases  of the headers are actually not installed.  However I can see the “missing” headers in /Library/Developer/CommandLineTools/usr/include/c++/v1 but I’m not sure this is place R is looking (information on the web is sometimes dated, and Apple seems to have moved things around in recent versions).  So my best guess is that R is looking elsewhere or doesn’t have a link to the correct location.  R Installation and Administration doesn’t appear to spell the location or I missed it.

I have carefully uninstalled Xcode (13) and re-installed it, and run Xcode-select —install (it thinks the CLTs are already installed).  This does not make any difference, the problem persists.  Restarting the machine after updates does not make a difference either.

Thanks for any suggestions, as I’m really stuck...

Bryan


> sessionInfo()
R version 4.1.1 Patched (2021-10-18 r81073)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
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  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.1.1