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

[Bryan Hanson]

Thank you Simon, that was spot-on!  There was a stale Makevars file from about a year ago when a particular package needed a kluge to compile with openMP.  Much appreciated!  Bryan

> On Oct 22, 2021, at 3:54 PM, Simon Urbanek <simon.urbanek using R-project.org> wrote:
> 
> Bryan,
> 
> you seen to be using non-standard compiler in /usr/local/clang4. Remove it and check you overrides - do you have some forgotten invalid ~/.R/Makeconf file? Remove those if you do - and check ~/.R for any old stuff. (In fact the latter will probably fix it alone).
> 
> Cheers,
> Simon
> 
> 
> 
>> On Oct 23, 2021, at 11:29 AM, Bryan Hanson <hanson using depauw.edu> wrote:
>> 
>> 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
>> 
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>