Having a recurring issue with cmath upon compiling the source R package in OSX 10.15, as follows;
In file included from /usr/local/opt/llvm/bin/../include/c++/v1/complex:245:
/usr/local/opt/llvm/bin/../include/c++/v1/cmath:313:9: error: no member named 'signbit' in the global namespace
using ::signbit;
~~^
/usr/local/opt/llvm/bin/../include/c++/v1/cmath:314:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
~~^
/usr/local/opt/llvm/bin/../include/c++/v1/cmath:315:9: error: no member named 'isfinite' in the global namespace; did you mean 'finite'?
using ::isfinite;
~~^
/usr/local/include/math.h:749:12: note: 'finite' declared here
extern int finite(double)
Installation output from R shows clang++ with following arguments;
clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.6.2/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Library/R/3.x/library/BH/include" -I"/Volumes/Documents/Library/R/3.x/library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pipe -Wno-nonnull -pedantic -std=c++11 -mtune=native -c AlphaProcedure.cpp -o AlphaProcedure.o
I've read several similar posting having the similar issues but none of workaround has worked on my system so far. I'd really appreciate any input on this.
My system:
sw_vers ProductName: Mac OS X ProductVersion: 10.15.2 BuildVersion: 19C57
xcodebuild -version
Xcode 11.3
Build version 11C29
clang -v
clang version 9.0.0 (tags/RELEASE_900/final)
Target: x86_64-apple-darwin19.2.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin
gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/9.2.0_3/libexec/gcc/x86_64-apple-darwin19/9.2.0/lto-wrapper
Target: x86_64-apple-darwin19
Configured with: ../configure --build=x86_64-apple-darwin19 --prefix=/usr/local/Cellar/gcc/9.2.0_3 --libdir=/usr/local/Cellar/gcc/9.2.0_3/lib/gcc/9 --disable-nls --enable-checking=release --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-9 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --with-pkgversion='Homebrew GCC 9.2.0_3' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --disable-multilib --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
Thread model: posix
gcc version 9.2.0 (Homebrew GCC 9.2.0_3)
C complier flags in zshrc
CPATH=/usr/local/include
CPPFLAGS=-I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include
SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
LDFLAGS=-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib
Makevars (for R)
LLVM_LOC = /usr/local/opt/llvm
CC=clang -fopenmp
CXX=clang++ -foropenmp
CXX11=clang++ -fopenmp
CFLAGS = -g -O3 -Wall -pipe -pedantic -Wno-nonnull -std=gnu99 -mtune=native -pipe
CXXFLAGS = -g -O3 -Wall -pipe -Wno-nonnull -pedantic -std=c++11 -mtune=native
CXX11FLAGS = -g -O3 -Wall -pipe -Wno-nonnull -pedantic -std=c++11 -mtune=native
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include
I took the nuclear option (clean install Catalina) and used llvm provided by Apple with Brew installation of some required apps. All of this fixed the issue. One minor fix is in Makevars with CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include