I've got the same issue yesterday. My Update Manager listed some abrowser and linux-kernel updates so I wanted to upgrade however my root partition was full so I closed the application beforehand, cleared my APT cache, and then restarted the app again. But this time the manager was greyed out and unresponsive so I was forced to end it via System Monitor.

I eventually fixed this problem by using Synaptic where the update went smoothly (except that the torproject repository key signature was expired, so I needed to disable it first). Today I've got three gnome-control-center related updates and I was able to upgrade with the Update Manager without problems.

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