No by build system I mean whatever method you use to build the application on the host system - "make" would be a typical build system, but there are people who write shell-scripts or some such to compile their code. Since I am not familiar with the actual application you are trying to build, I can't say how it is being built.
If it's using make, then it probably means you have to define CC (or CXX) to match your cross-compiler. In other variants of build system, you would have to do somehting similar, but it's hard to describe without being familiar with that particular build-system.
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Mats
