compiler.link_executable doesn't find headers in /usr/local/include

An attempt to find fftw3.h in /usr/local/include on FreeBSD here https://github.com/pavlin-policar/fastTSNE/blob/master/setup.py#L51 fails because compiler.link_executable doesn't use CFLAGS.
This link suggests that CFLAGS environment variable should be sufficient: https://stackoverflow.com/questions/6928110/how-may-i-override-the-compiler-gcc-flags-that-setup-py-uses-by-default

Environment does contain CFLAGS:

XDG_DATA_HOME=/usr/ports/biology/py-fastTSNE/work-py36 XDG_CONFIG_HOME=/usr/ports/biology/py-fastTSNE/work-py36 HOME=/usr/ports/biology/py-fastTSNE/work-py36 PATH=/usr/ports/biology/py-fastTSNE/work-py36/.bin:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fno-omit-frame-pointer -fstack-protector -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-fno-omit-frame-pointer -isystem /usr/local/include" LDFLAGS=" -fstack-protector -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-omit-frame-pointer -fstack-protector -isystem /usr/local/include -fno-strict-aliasing -fno-omit-frame-pointer -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"

Yet:

===>  Building for py36-fastTSNE-0.2.13
./tmpyibjm545/fftw3..c:1:10: fatal error: 'fftw3.h' file not found
#include <fftw3.h>
         ^~~~~~~~~

Reference issue: https://github.com/pavlin-policar/fastTSNE/issues/43

FreeBSD 11.2, port infrastructure.

Start at compiler.link_executable and inspect how the shown CFLAGS and CPPFLAGS reach header compilation. Reproduce the fftw3.h failure with the referenced fastTSNE setup.py on FreeBSD. Done means the compiler can find headers in /usr/local/include using the environment flags.