Error when with Xcode 5.0 and Rcpp (Command Line Tools ARE installed)

I'm not sure what you mean by "I downloaded a gcc compiler". You don't need to download your own gcc. You can use either the default or use clang++ by having something like this in your ~/.R/Makevars file:

CC=clangCXX=clang++CXXFLAGS= -O3 -pedantic

What happens when you try devtools::has_devel:

> require(devtools)> has_devel()'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD SHLIB foo.cclang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c foo.c -o foo.oclang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o foo.so foo.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation[1] TRUE

or Rcpp::evalCpp:

> require(Rcpp)> evalCpp( "1+1")[1] 2    

Quick guess:

1. You are running the pre-built R binary which Simon built / CRAN provides.

2. R stores its configuration options from its compile time, those influence its run-time.

3. Check via the file $R_HOME/etc/Makeconf and look at CC and CXX.

4. As Romain suggested, override CC and CXX via a file ~/.R/Makevars.

5. Try again.

Edit: I just confirmed with a colleague who has the exact same issue on a Mac OS X whichhe just upgrades to XCode 5 -- one now needs to override CC and CXX as R was built with the previous version of XCode.

A easier solution would be the following.You should soft link the llvm compiler, in the terminal type:

cd /usr/binsudo ln -fs clang llvm-gcc-4.2sudo ln -fs clang++ llvm-g++-4.2

Note: This also works for mex in Matlab.