I don't want the system to shutdown in the middle of the upgrade, but I've already started the upgrade in the GUI.

Is there a better way, maybe involving the apt lock?

EDIT: Thank you for all the helpful suggestions. Hopefully this helps the next person. My upgrade actually finished on its own while I was posting. ๐Ÿ˜‚

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[โ€“] 4 points 4 months ago

No, the idea was that apt update would keep failing while the system upgrade was running (and holding the lock):

$ apt update
E: Could not get lock /var/lib/apt/lists/lock. It is held by process 1704856 (apt)
N: Be aware that removing the lock file is not a solution and may break your system.
E: Unable to lock directory /var/lib/apt/lists/

But there are better ways of waiting for a process to finish, that other people have shared

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