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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