Since I installed Catalina, any attempt to compile an R package fails. My system is set up to use home-brew. The failure messages look like this:
/usr/local/clang8/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I/usr/local/clang8/include -I/usr/local/Cellar/gcc/8.3.0_2/include -fopenmp -fPIC -Wall -g -O2 -c R_register_native.c -o R_register_native.o
In file included from R_register_native.c:1:
/Library/Frameworks/R.framework/Resources/include/R.h:55:11: fatal error: 'stdlib.h' file not found
# include <stdlib.h> /* Not used by R itself, but widely assumed in packages */
After googling I found this link in the home-brew site on GitHub. I can't follow much of the discussion but it seems that Apple removed the usr/include directory and that the home-brew folks are looking for a solution. I don't immediately have a need to compile these packages so my plan is to wait until home-brew finds a solution. But if there is an easy one now, please share.
After some additional searching I found this link with a bunch of discussion about this problem, a lot of which I didn't understand. But this bit of code seemed promising.
sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/* /usr/local/include/
I ran it, rebooted my mac, opened RStudio and got the list of new package updates. Ran the update, answering yes to compile. Lots of messages and some warnings but at the end of it all, there were no errors. But all the messages start with something like
/usr/local/clang8/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I/usr/local/clang8/include -I/usr/local/Cellar/gcc/8.3.0_2/include -fopenmp -fPIC -Wall -g -O2 -c R_register_native.c -o R_register_native.o
When I cd into /usr/local/clang8/bin and get the version of clang it is Apple clang version 11.0.0. Also clang symlinks to clang-8 and clang++ symlinks to clang
The contents of /usr/local/Cellar/gcc is a directory called 9.2.0_1. When I go to /usr/bin and run gcc --version I get messages about this being Apple clang version 11.0.0. It seems like R is compiling using the Apple clang version. Is that a problem? Is there some way to move everything to using the brew version of clang? FYI, here's my current path - /usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin:/Library/Apple/bin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/CrossPack-AVR/bin:/usr/local/git/bin
