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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.
Cmake also contain a lot of Find* [modules](https://cmake.org/cmake/help/v3.9/manual/cmake-modules.7.html) 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](https://cmake.org/cmake/help/v3.9/module/FindOpenGL.html) and [FindSDL](https://cmake.org/cmake/help/v3.9/module/FindSDL.html) 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.