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When Kibana is installed with the ES repository, Kibana will be updated when running apt upgrade. Even though this is very convenient and simple to do, Kibana won't start after the update for two reasons:
1. the newly installed binaries are installed as root user - therefore they are owned by root:root and the user kibana cannot execute it
2. The new installation is lacking the permission to run on the default http/ https ports.
As root or with sudo run:
chown -R kibana:kibana /usr/share/kibana setcap cap_net_bind_service=+epi /usr/share/kibana/bin/kibana setcap cap_net_bind_service=+epi /usr/share/kibana/bin/kibana-plugin setcap cap_net_bind_service=+epi /usr/share/kibana/bin/kibana-keystore setcap cap_net_bind_service=+epi /usr/share/kibana/node/bin/node