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I am using ROS2 Foxy. I also see these two lines
RosPluginProvider._parse_plugin_xml() plugin file "C:\dev\ros2-windows\share\rqt_gui_cpp/plugin.xml" in package "rqt_gui_cpp" not found
RosPluginProvider._parse_plugin_xml() plugin file "C:\dev\ros2-windows\share\rqt_gui_cpp/plugin.xml" in package "rqt_gui_cpp" not found
But my rqt_graph opens and runs properly. So I just ignored the message. Make sure you run dot -c from the admin cmd prompt before running rqt_graph for the first time. ROS2 is in heavy development so if the problem persists you can switch to Foxy and check out the new version. Maybe the problem that you mentioned has been solved in the latest ros2 distro.
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