MacOS min version needed for GCC compiler on Monterey

September 19, 2022 by Kinh Nguyen

A note to fix error on new MacOS version Monterey and gcc compiler for R. This assumes that you have

Install Xcode Command Line Tools
Install new gfortran version from here.

Then when running pkgbuild::check_build_tools(debug = TRUE) you might see

ld: library not found for -lSystem
clang-5.0: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [foo.so] Error 1
Error: Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.

in ~/.R/Makevars add the following to the CC and CCX

CC=ccache /usr/local/gfortran/bin/gcc -mmacosx-version-min=12.3 -fopenmp
CXX=ccache /usr/local/gfortran/bin/g++ -mmacosx-version-min=12.3 -fopenmp

Running and it works for me.

> pkgbuild::check_build_tools(debug = TRUE)
Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c

ccache /usr/local/gfortran/bin/gcc -mmacosx-version-min=12.3 -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/usr/local/Cellar/gperftools/2.9.1_1/include/gperftools   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c foo.c -o foo.o

ccache /usr/local/gfortran/bin/gcc -mmacosx-version-min=12.3 -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -I/usr/local/Cellar/gperftools/2.9.1_1/lib -F/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/ -o foo.so foo.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

ld: warning: -undefined dynamic_lookup may not work with chained fixups
 
Your system is ready to build packages!

A complete Makevars is below, please adjust your path accordingly, especially FLIBS and MAC_LOC. I also have gperftools and ccache install so remove them if you don’t need them.

FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin21/12.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm

CC=ccache /usr/local/gfortran/bin/gcc -mmacosx-version-min=12.3 -fopenmp
CXX=ccache /usr/local/gfortran/bin/g++ -mmacosx-version-min=12.3 -fopenmp
CXX11=ccache /usr/local/gfortran/bin/g++ -mmacosx-version-min=12.3 - fopenmp
CXX17=ccache /usr/local/gfortran/bin/g++ -mmacosx-version-min=12.3 - fopenmp

LLVM_LOC=/usr/local/opt/llvm
MAC_LOC=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
GPLOC=/usr/local/Cellar/gperftools/2.9.1_1
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -Wno-ignored-attributes -Wno-maybe-uninitialized
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib -I$(GPLOC)/lib -F/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/System/Library/Frameworks/
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I$(MAC_LOC) -I$(GPLOC)/include/gperftools

Comments