It slows there machine to a crawl infact at some point you cannt move the mouse or type.
In /etc/make.conf, increase portage niceness so that it runs with less priority.
I was thinking of adding update as a cron job and just do it every night at midnight.
Does a desktop system really need the latest and greatest software versions every night? Doing it every day will require more updates than the current rate will, because more than one new version of the same software might come out in those two weeks. If you get emerge to run so it doesnt slow the system down as much, a bigger update might be more doable anyway.
My problem is there are three things im worried about, first how likly do you think compiling will break something?
Not that often, unless you're using ~x86 (or heaven forbid -x86

), but what happens if a compile failes during your auto-update? The rest of the update won't complete, and you'll be left with the old version (it won't be broken, just it won't be updated).
They dont reboot often so what if there still running the old version in memory while theres a new version on there system?
I'd say theres a lot more applications than system software. In other words, services, daemons etc. wont use the new version until the machine is rebooted, but other stuff like browsers, word processors etc. will start the new version the next time it is run.
Thrid what about etc-update what if I just let them build up for like two weeks, is it really THAT horrible?
Well, if a program gets updated and the config files are not updated by etc-update, then what if the new version of the program requires something in the new config file, but its not there in the old one? I would say its best to etc-update straight after an emerge. And don't event
think of having etc-update run automatically...
If you ask me, I'd say to
- Set portage niceness so you can emerge without having it hog the system
- and by all means put 'emerge sync && emerge -uf world' in a cron job (to run once a week maybe) so that when you turn up, updates are already downloaded and ready to compile.
I think it'd be best if you were there to etc-update and sort out failed emerges or other problems with new versions...
Of course, you could allways remote-manage the PC. Maybe run an ssh daemon (with airtight security of course) and tunnel into their PC from home, do their emerge -u world, etc-update and reboot remotely.

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