Ralf, thank you! Your advice is making sense.
However, I find that installation on macOS fails when I have this in src/Makevars:
CXX_STD = CXX11
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o harmony.so RcppExports.o harmony.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [harmony.so] Error 1
ERROR: compilation failed for package ‘harmony’
I find that macOS has no problem with installation when the src/Makevars is empty.
So, it seems that I may need to have one Makevars for macOS, and a different Makevars for Linux.
I'm still scratching my head about how to get this right.
Could I please ask if you know the right way to do this?