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Problem with sourcing setup.bash

Hi, I have some packages installed with apt, and some from from source in catkin_ws. The problem Im having is that the source /opt/ros/kinetic/setup.bash file and the ~/catkin_ws/devel/setup.bash file conflicts. As soon as I source catkin I can not find some packages In opt/ros, and as soon as I source opt/ros I can not find any of my catkin nodes. I have been struggling with this for a while now and Im wondering if it is a way of resolving this conflict?