Kevin has a good point, there is likely a lot more messed up in your system. A good way to restore normality is something like:
sudo -i cd /usr/local mkdir .disable mv * .disable/ Things should work then. You can undo the above with something like sudo -i cd /usr/local mv .disable/* . rmdir .disable On older macOS versions it was so much easier since you could simple rename /usr/local but Apple doesn't want us to do such simple things anymore ... Cheers, Simon > On Dec 3, 2021, at 12:32 PM, Kevin Ushey <kevinus...@gmail.com> wrote: > > This may also make your life challenging: > > /usr/local/include/sys/_types.h:33:10: fatal error: 'machine/_types.h' file > not found > #include <machine/_types.h> > ^~~~~~~~~~~~~~~~~~ > 1 error generated. > > You have some headers installed in /usr/local/include that are > shadowing the default macOS toolchain's headers, and those appear to > be incompatible with the system toolchain. You'll likely need to > remove those as well. > > To be complete, x86_64 builds of R usually have something like: > > CPPFLAGS = -I/usr/local/include > > within their Makeconf; if you've placed headers there that shadow the > default system headers, they'll be used instead. > > tl;dr: you probably need to do a couple things. > > (1) Remove /usr/local/opt/llvm/bin from your PATH so llvm clang stops > shadowing the system clang; > (2) Remove the system headers in /usr/local/include that are masking > your system header includes. > > You could also probably force the use of system clang in R by setting > CC = /usr/bin/clang and CXX = /usr/bin/clang++ in (say) ~/.R/Makevars, > but I haven't tried that. > > Best, > Kevin > > On Thu, Dec 2, 2021 at 1:29 PM Simon Urbanek > <simon.urba...@r-project.org> wrote: >> >> >> Adrian, >> >> >>> On Dec 3, 2021, at 10:12 AM, Adrian Dușa <dusa.adr...@gmail.com> wrote: >>> >>> Thank you Simon, >>> >>> I have the official Apple CLT, but not the full Xcode. If needed I can >>> install that as well, with a difference of about 10GB more space getting >>> used. >>> This is what I get: >>> >>> $ xcode-select -p >>> /Library/Developer/CommandLineTools >>> >>> $ xcrun --show-sdk-path >>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk >>> >>> $ which clang >>> /usr/local/opt/llvm/bin/clang >>> >> >> >> ^^^-- this is your problem. You're not using Xcode so that's exactly what I >> said, you have a broken compiler. Remove /usr/local/opt and it should work. >> >> Cheers, >> Simon >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
