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Make sure you are cloning the repository inside the src folder of your workspace. For instance, if your workspace is called catkin_ws and that folder resides in your home directory, then the place to clone your repository is ~/catkin_ws/src. Then you have to invoke catkin_make from inside catkin_ws and not catkin_ws/src.

I suggest that you use catkin build instead. I find it nicer and you can invoke it from within any subfolder of your workspace. I like to think that it works somewhat like git in that particular respect: works from any subfolder.