Source Cpp file failed due to math.h not found

[yangleicq]

Recently, I updated my mac to macOS Mojave Version (10.14.1). After that Rcpp cannot build from source. For the example below, "example.cpp" is just the template code created by Rstudio.

Rcpp::sourceCpp('Documents/example.cpp')
In file included from example.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/r/headers.h:59:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
In file included from /usr/local/clang4/bin/../include/c++/v1/cmath:305:
/usr/local/clang4/bin/../include/c++/v1/math.h:301:15: fatal error: 'math.h' file not found
#include_next <math.h>
              ^~~~~~~~
1 error generated.
make: *** [example.o] Error 1
/usr/local/clang4/bin/clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Users/yangleicq/Documents/" -I/usr/local/include   -fPIC  -Wall -g -O2  -c example.cpp -o example.o
Error in Rcpp::sourceCpp("Documents/example.cpp") : 
  Error 1 occurred building shared library.

I check the "/usr/local/clang4/bin/../include/c++/v1/math.h", it definitely is there.
I read the issue from coatless-mac/r-macos-clang#10 (comment), and followed the instruction to run xcode-select --install and sudo xcodebuild -license accept, still ran into the same error message. I reinstalled R, Rcpp, Xcode, still the the same error message.

Finally I changed CXX=/usr/local/clang4/bin/clang++ to CXX=g++ in ~/.R/Makevars, and the error message is gone. Basically I can only change the compiler to make things work.

[coatless]

@yangleicq c.f. coatless-mac/r-macos-rtools#11 (comment)

On Mojave use:

sudo installer -pkg \
/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg \
-target /

@eddelbuettel please close.

[yangleicq]

Thank you, it works.

[kklot]

Does not work for me, installed

installer: Package name is macOS_SDK_headers_for_macOS_10.14
installer: Installing at base path /
installer: The install was successful.

restarted R, restarted Mac

/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:10: fatal error: 'cmath' file not found

[eddelbuettel]

So your ducks are not in a row. See the Rcpp FAQ vignette. Ask for help on r-sig-mac. It works for CRAN on macOS too, as it does for thousands of users.

[glennmschultz]

Running into the same problem on Catalina OS. Does the recommend fix for Mojave work as well just replace the build number?

[eddelbuettel]

Not a macOS user myself but there were a number of posts on StackOverflow too once Catalina was released. As I recall, you need to reinstall some tools. This thread is not the best reference so I recommend we do not continue here.

[kevinushey]

Unfortunately, those instructions are no longer relevant for macOS Catalona. See the guide @coatless has put together:

https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/

Note also that the issue is handled by R itself in the recent patch releases of R 3.6.1 as well. If you're aggressively updating your OS, you should be aggressively updating your other software as well.

Locking this thread for now as it is indeed not the best avenue for discussion.