I have almost completely borked my laptop. Let me start by saying it is definately a configuration issue, because everything works fine with a live CD. Almost everything works as root, which is why I've puzzled (it should be much closer to "everything works as root"). This is Dapper, BTW.

The last thing I did when it broke.

I was installing the dynamic DNS client from no-ip.com. I had done this before on my desktop several months ago and I was putting it on my laptop. I did the whole `make ; sudo checkinstall` dance. During the checkinstall, it asked which network interface to use. The one I wanted (eth0) was not up at the time, so I ctrl-C'ed the install and then things went south. I suddenly couldn't run anything as a normal user. I tried switching to the console but the lame ATI drivers hung as they are wont to do. So did a hard reboot and the laptop booted into the console (no gdm). I have a root password and I can do most things as root.

Symptoms

gdm doesn't work. However, startx as root works.

sudo doesn't work, even as root. It complains about not having permissions for /etc/sudoers, yet if I chmod them it complains about incorrect permissions.

I can't do anything as a non-root user. I have tried login, su, sudo, even local ssh (I think it just uses login), all to no avail. login complains about not being able to cd to /home/username. su simply says "No shell". See above for sudo. ssh behaves like login. I have tried this for two different "real" (i.e. general purpose, you can get work done with them) users. I made a third user just to test with. I tried starting the folding@home daemon, which runs as its own user, and it always fails. /home (and everything else) mounts properly.

dbus is broken. hal fails to startup properly. I'm not that familiar with what exactly dbus is, so I'll leave it at that.

The network won't come up. I get errors from dhcdbd about dbus_svc_init in /var/log/syslog. I get permission errors from /lib/dhcp3-client/call-dhclient-script.

Logs

/var/log/syslog
List of files modified since the disaster.
Generated with /var/log/auth.log
Research

Some related threads:

http://ubuntuforums.org/showthread.php?t=405942
http://ubuntuforums.org/showthread.php?t=406895

Plans

I'm going to do some more tests, and then probably just install Feisty since it is so close to being released and I was going to update this month anyway. I would really like to know what is going on. If anyone has any ideas, I will not reinstall until we try them out. This laptop is not essential for my work, but is inconvenient to have it not working.

Could anyone tell me how to enable the universe repo? Thanks.

My problems were definately caused by noip's client and/or checkinstall. I can reproduce the problem with a live CD.

I boot the live CD (Xubuntu Dapper in this case), and do the following:
During checkinstall, I answer yes to the package docs question, then ctrl-C. Trying to run any command as the ubuntu user results in a permission error. Permission is denied for /etc/sudoers, even as root. Network is still up.

Edit:
The traditional "make install" causes no trouble.

It seems like this bug got fixed somewhere in the time between Dapper and Feisty. I just tried to reproduce in Feisty under VMware, and it doesn't trash the system. Clearly checkinstall has gone through some updates because it 1f40 no longer depends upon installwatch. Anyway, checkinstall still fails because it can't copy the binary or something like that, but make install still works.

I suppose the lesson is be careful with checkinstall, which is too bad because I really like that program. I've used it many times, but usually with programs using the GNU build system (./configure && make && make install), and this thing was definately not using that. I think the problem was that it started asking questions.

I'd still really like to know what the hell caused all the permission problems.