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The behaviour your are observing has to do with how catkin workspaces are chained.

At the time you created your catkin workspace, other workspaces had already been created and sourced within the shell you were using.

A quick fix (if you only want to have the system-wide installed ROS packages and your catkin workspace sourced) is:

cd your_catkin_ws/src
rm -rf build/ devel/
cd your_catkin_ws/src
rm CMakeLists.txt
source /opt/ros/hydro/setup.bash
catkin_init_workspace
cd your_catkin_ws
catkin_make

Then, remember to have only one line in your .bashrc:

source path_to_your_catkin_ws/devel/setup.bash

See the answers (particularly the second one) to this question for a more detailed explanation on how chaining of catkin workspaces actually works.

The behaviour your are observing has to do with how catkin workspaces are chained.

At the time you created your catkin workspace, other workspaces had already been created and sourced within the shell you were using.

A quick fix (if you only want to have the system-wide installed ROS packages and your catkin workspace sourced) is:

cd your_catkin_ws/src
your_catkin_ws/
rm -rf build/ devel/
cd your_catkin_ws/src
rm CMakeLists.txt
source /opt/ros/hydro/setup.bash
catkin_init_workspace
cd your_catkin_ws
catkin_make

Then, remember to have only one line in your .bashrc:

source path_to_your_catkin_ws/devel/setup.bash

See the answers (particularly the second one) to this question for a more detailed explanation on how chaining of catkin workspaces actually works.