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So the CMakeLists.txt in the directory of your ROS package (ie: not the catkin_ws/src directory) is a symlink to /opt/ros/kinetic/share/catkin/cmake/catkin_package.cmake?

If yes: yes, that would be a problem.

So the CMakeLists.txt in the directory of your ROS package (ie: not the catkin_ws/src directory) is a symlink to /opt/ros/kinetic/share/catkin/cmake/catkin_package.cmake?

If yes: yes, that would be a problem.

mkdir -p /tmp/abcd/catkin_ws/src
cd /tmp/abcd/catkin_ws
source /opt/ros/kinetic/setup.bash
catkin_make

mkdir -p /tmp/efgh/catkin_ws/src
cd /tmp/efgh/catkin_ws/src
source /opt/ros/kinetic/setup.bash
catkin_create_pkg bar_pkg roscpp
cd /tmp/efgh/catkin_ws
catkin_make

tree -L 2 /tmp/efgh/catkin_ws/src

So the CMakeLists.txt in the directory of your ROS package (ie: not the catkin_ws/src directory) is a symlink to /opt/ros/kinetic/share/catkin/cmake/catkin_package.cmake?

If yes: yes, that would be a problem.

Edit: Ok. One final check.

Open $HOME/.bashrc. Scroll to the end. Make sure there are no source lines that source any workspaces. Not even /opt/ros. If there are, comment them (#) then save the file.

Now open a new terminal and run this:

mkdir -p /tmp/abcd/catkin_ws/src
cd /tmp/abcd/catkin_ws
source /opt/ros/kinetic/setup.bash
catkin_make

Does that build successfully?

If it does, again open a new terminal, then:

mkdir -p /tmp/efgh/catkin_ws/src
cd /tmp/efgh/catkin_ws/src
source /opt/ros/kinetic/setup.bash
catkin_create_pkg bar_pkg roscpp
cd /tmp/efgh/catkin_ws
catkin_make

Finally, show us the output of:

sudo apt install -y tree
tree -L 2 /tmp/efgh/catkin_ws/src