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In your manifest.xml, you probably have the following line:

<rosdep name="joint_state_publisher"/>

This is incorrect; instead, change it to:

<depend package="joint_state_publisher"/>

The reason is that rosdep checks for system dependencies (i.e., non-ROS software that is available as a debian package, like libmesa or qt4-qmake). On the other hand, rospack (which is invoked by the depend tag) is responsible for finding ROS package dependencies.