$ ./fltk-config --compile foo.cxx
/Library/Developer/CommandLineTools/usr/bin/c++ -I/usr/local/src/fltk-1.4.x-git/build -I/usr/local/src/fltk-1.4.x-git -isysroot -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_THREAD_SAFE -D_REENTRANT -o 'foo' 'foo.cxx' /usr/local/src/fltk-1.4.x-git/build/lib/libfltk.a -lm -lpthread -framework Cocoa
clang: warning: no such sysroot directory: '-D_LARGEFILE_SOURCE' <-- NOT EXPECTED
foo.cxx:1:10: fatal error: 'stdio.h' file not found <--
#include <stdio.h> <--
^
1 error generated.

This error arises because the command line contains option "-isysroot" not followed by a proper SDK path.

That path is normally computed by cmake when it runs in its variable CMAKE_OSX_SYSROOT (see clip below).

Greg: don't you see that variable being assigned a value when you run cmake on macOS?

The statement at line #59 of file CMake/options.cmake is

  list (APPEND FLTK_CFLAGS "-isysroot ${CMAKE_OSX_SYSROOT}")
and this contributes to the value of CXXFLAGS at line #46 of file fltk-config which is expected to contain

"-isysroot" followed by the path to the SDK adequate for the running system.