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If you're using a REP 117 compliant laser/driver, like the hokuyo_node, you must use navigation +1.11.5 and pass the inf_is_valid param to your global and local costmap configuration. Otherwise, when the laser doesn't see anything you'll have +Inf, and they're not converted from LaserScan to PC in the costmap_2d code, and consequently nothing is cleared.

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