Likewise no problems compiling using an older version of clang (Xcode 5.0.2), but I do see that flag
bizarro% clang --version Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) Target: x86_64-apple-darwin13.3.0 Thread model: posix It looks like it's in there. There is a test to check (see below) but the compiler doesn't fail, it just warns so the test is perhaps concluding that yep, supported which is technically true. bizarro% find . -type f -exec grep malign-double {} /dev/null \; ... ./deps/fftw-3.3.3-double/config.log:clang: warning: argument unused during compilation: '-malign-double' ./deps/fftw-3.3.3-double/config.log:configure:14242: clang -stdlib=libc++ -mmacosx-version-min=10.7 -m64 -c -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math ... ./deps/fftw-3.3.3-single/configure:$as_echo_n "checking whether C compiler accepts -malign-double... " >&6; } ./deps/fftw-3.3.3-single/configure: CFLAGS="-malign-double" ./deps/fftw-3.3.3-single/configure: CFLAGS="$CFLAGS -malign-double" ./deps/fftw-3.3.3-single/configure: # -malign-double for x86 systems ./deps/fftw-3.3.3-single/configure: { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts -malign-double" >&5 ./deps/fftw-3.3.3-single/configure:$as_echo_n "checking whether C compiler accepts -malign-double... " >&6; } ./deps/fftw-3.3.3-single/configure: CFLAGS="-malign-double" ./deps/fftw-3.3.3-single/configure: CFLAGS="$CFLAGS -malign-double" ./deps/fftw-3.3.3-single/configure: { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts -malign-double" >&5 ./deps/fftw-3.3.3-single/configure:$as_echo_n "checking whether C compiler accepts -malign-double... " >&6; } ./deps/fftw-3.3.3-single/configure: CFLAGS="-malign-double" ./deps/fftw-3.3.3-single/configure: CFLAGS="$CFLAGS -malign-double" ... Binary file ./usr/lib/libfftw3.3.dylib matches Binary file ./usr/lib/libfftw3.a matches Binary file ./usr/lib/libfftw3f.3.dylib matches Binary file ./usr/lib/libfftw3f.a matches