Rcpp package doesn't run R 3.6 MacOS Mojave.

I've got the following error when I run


evalCpp("2 + 2")

The output is:

clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/private/var/folders/h5/r7lh__p16wx7cg_5pzknfg5w0000gn/T/Rtmpz3QxlQ/sourceCpp-x86_64-apple-darwin15.6.0-1.0.1" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c file7d712a4a950.cpp -o file7d712a4a950.o
Error in sourceCpp(code = code, env = env, rebuild = rebuild, cacheDir = cacheDir,  : 
  Error 1 occurred building shared library.
clang: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot]
In file included from file7d712a4a950.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:59:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:305:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/math.h:301:15: fatal error: 'math.h' file not found
#include_next <math.h>
1 error generated.
make: *** [file7d712a4a950.o] Error 1
  • What research have you done? What have you tried so far to fix this? Jun 3, 2019 at 21:49
  • I tried to downgrade R version but I've failed. I did google research about the clang stuff with no results. I´m not a lazy one music2myear Jun 3, 2019 at 21:53

2 Answers 2


macOS 10.14 does not install its header files in the old location anymore. Many third-party installations are broken unless you run:

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

See also this GitHub issue.

You have to repeat this command when updating R or macOS (Xcode).

  • Works for me. I had to install the package directly from Apple developers website. Regards Jun 3, 2019 at 14:13

Another solution that does not require forced installation of headers in their old location is to tell R their new location by setting the following variables in ~/.R/Makevars:

CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

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

  • 1
    Just to add those three lines didn't work for me. I had to follow the whole procedure outlined in the link above for installing R COMPILER TOOLS FOR RCPP ON MACOS. (thecoatlessprofessor.com/programming/cpp/…). But then it worked like a charm! +1 from me
    – petzi
    Oct 26, 2019 at 12:19

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