Compile issue with Rstan on Macbook Pro M1

Interfaces RStan
, ,
11

Thanks for all the help. I also have an unsolved issue. Also originally here: Can't compile code using RStan

Here’s the full error now. I reinstalled everything including CommandLineTools. I really don’t know what the problem is.

> brm(mpg~1,mtcars)
Compiling Stan program...
make cmd is
  make -f '/Library/Frameworks/R.framework/Resources/etc/Makeconf' -f '/Library/Frameworks/R.framework/Resources/share/make/shlib.mk' -f '/Users/justinsavoie/.R/Makevars' CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB='file18ab72d229a7.so' OBJECTS='file18ab72d229a7.o'

make would use
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include    -fPIC  -O3 -fPIC -c file18ab72d229a7.cpp -o file18ab72d229a7.o
if test  "zfile18ab72d229a7.o" != "z"; then \
	  echo clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o file18ab72d229a7.so file18ab72d229a7.o  '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/lib//libStanServices.a' -L'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/lib/' -lStanHeaders -L'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/lib/' -ltbb   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation; \
	  clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o file18ab72d229a7.so file18ab72d229a7.o  '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/lib//libStanServices.a' -L'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/lib/' -lStanHeaders -L'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/lib/' -ltbb   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation; \
	fi
Error in compileCode(f, code, language = language, verbose = verbose) : 
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstring:66:5: error: <cstring> tried including <string.h> but didn't find libc++'s <string.h> header.           This usually means that your header search paths are not configured properly.           The header search paths should contain the C++ Standard Library headers before           any C Standard Library, and you are probably using compiler flags that make that           not be the case.#   error <cstring> tried including <string.h> but didn't find libc++'s <string.h> header. \    ^fatal error: too many errors emitted, stopping now [-ferror-limit=]20 errors generated.make: *** [file18ab72d229a7.o] Error 1
Error in sink(type = "output") : invalid connection

I have Sonoma 14.0 (23A344).
I have xcode-select version 2399.

Additionally:

g++ --version
Apple clang version 15.0.0 (clang-1500.0.40.1)
Target: arm64-apple-darwin23.0.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

I found this here: ⚙ D131441 [libc++] Diagnose when header search paths are set up incorrectly which says "For example, people will manually add -isystem /usr/include, which ends up messing up the layering of header search paths required by libc++ (because the C Standard Library now appears before libc++ in
the search paths). " but I still don’t know how to fix it.

At the end of the day it’s probably this: “The header search paths should contain the C++ Standard Library headers before any C Standard Library, and you are probably using compiler flags that make that not be the case.” but again; not sure.