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I was having the same problem. I closed everything, run rqt --force-discover and then everything was working. I run it with rosrun rqt_graphprofiler rqt_graphprofiler and now it also appears under Instrospection plugins.
However, I cannot see anything in the window. No graph is shown.
$ cat /etc/issue
Ubuntu 14.04.1 LTS \n \l
$ sudo apt-get install ros-indigo-rqt-graphprofiler
$ which rqt_graphprofiler
/opt/ros/indigo/bin/rqt_graphprofiler
$ rqt_graphprofiler
qt_gui_main() found no plugin matching "rqt_graphprofiler.visualizer_plugin.VisualizerPlugin"
$ aptitude search rqt
i A ros-indigo-rqt-rviz
The graph profiler doesn't show up as a plugin in rqt either; perhaps it's related.
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