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

[Simon Urbanek]

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 <kevinushey using 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.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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