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Running Mint 18.2, Using propietary Nvidia driver. I'm compiling using SDL2 (which required me to install some Mesa libraries) if it's any help.
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Cmake also contain a lot of Find* modules specifically for detecting and locating libraries and dependencies. (basically independent of what platform or architecture Cmake tries to generate your project's Makefiles on).
Example is the FindOpenGL and FindSDL module.
It's also entirely possible to use Cmake to configure/write other files than Makefiles. And also to set and put environment vars into the generated Makefiles. Maybe it could be useful for your problem?
I apologize if i misunderstood your post though.