>From my duplicate bug #372460: This is probably due to this absurdly
small timeout in update-notifier-0.78/src/update-notifier.c:

#define TIMEOUT_APT_RUN 120 /* 120 sec */

Though even if the timeout expires, update-notifier should check to see
whether a package manager is still working, instead of advising the user
to immediately reboot which would forcefully abort the operation in
progress.

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update notifier tells you to reboot before the upgrade is complete
https://bugs.launchpad.net/bugs/274001
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