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I installed Python from sources

that is most likely the cause of the error you are seeing: sudo apt-get install python-catkin-pkg will install the distribution debian package, which places files in the normal locations, for the system Python.

Your from-source installed Python won't get those files, so when Catkin tries to use it to run some scripts, that interpreter will not be able to find what it needs.

You have two options:

1. make Catkin/CMake use the system Python
2. install the missing dependencies into the PYTHONPATH of your from-source Python installation

Option 1 is (probably) easy: remove your from-source Python from the PATH. Option 2 should also not be too difficult: use the pip of your from-source Python to install the necessary packages.

You might run into other problems with a non-system-default Python though, so if you don't really need it, it might pay to use the system Python instead.