Thanks again, problem solved. Removing llvm from /usr/local/opt does the trick.
Kevin's suggestion to have a Makevars file pointing to the system clang also worked, although I have no idea which headers from /usr/local/include are masking and which are not. I've removed all and get no more errors or warnings. Best wishes, Adrian On Fri, 3 Dec 2021 at 01:32, 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 > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac