For anyone attempting to compile code from an external source that uses an automated build utility such as Make, to avoid having to track down the explicit gcc compilation calls you can set an environment variable. Enter on command prompt or put in .bashrc (or .bash_profile on Mac):
export CFLAGS="-std=c99"
Note that a similar solution applies if you run into a similar scenario with C++ compilation that requires C++ 11, you can use:
export CXXFLAGS="-std=c++11"