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These might be some timing related issue. From what you write it looks a bit like the mapper is not able to provide the "map"->"odom" transformation in time. Please have a look at the system load (e.g. via the "System Monitor" or "top") to check if the mapper is unable to keep up. Also make sure that you use the "kinetic" branch of nav2d and that you build with -DCMAKE_BUILD_TYPE=Release.

If nothing of this helps, you could install the binary version of nav2d to see if it produces the same issues.

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