Cron is a spammer, how do I stop it?

Is the system running ouf of memory?

You can have a look in /var/log/syslog to see if you get any OOM (Out Of Memory) messages during the time of day when /etc/cron.daily/apt is running.

/etc/cron.daily/apt is executed at 06:25, but there is a random sleep in the apt script, so it might be up to 1800 seconds later

The command free -m will also be able to tell you how much free memory you have, and vmstat 5 will be able to show you if you have a lot of swapping, or memory movement going on.

If this is the case you might look into adding more swap, adding more memory, or find if you have any unnecessary processes running that takes all of your memory. (A reboot in the case of a memory leak)

Run apt manually?

Have you tried running /etc/cron.daily/apt manually to see if you can any more warnings/errors?

If you are running Ubuntu 14.04 LTS you'll find a call for random_sleep subroutine on line 425. Add a # on this line to not have it sleep before a run.

On Ubuntu 12.04 LTS it is line 423. Ubuntu 16.04 LTS should not have this file as far as I can see.

Run /etc/cron.daily/apt as root like this:

root@hostname:~# /etc/cron.daily/apt

Or with sudo like this:

username@hostname:~$ sudo /etc/cron.daily/apt

There might be some interesting errors to point to you the right direction, or try looking in the /var/log/syslog file for anything suspicious.