[R-SIG-Mac] unable to install from source packages needing compiled C code

[Kevin Ushey]

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.urbanek using r-project.org> wrote:
>
>
> Adrian,
>
>
> > On Dec 3, 2021, at 10:12 AM, Adrian Dușa <dusa.adrian using 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
>
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