[FIXED-ish] Updating: Pacman wants to remove /usr/

Question

error: cannot remove file '/usr/': Read-only file system
error: could not commit removal transaction
error failed to commit transaction (cannot remove all files for package)
Errors occurred, no packages were upgraded
Not sure why pacman wants to remove /usr... Also, /usr is not read-only, it's mounted as rw.
Last edited by Berticus (2009-02-08 20:15:45)

Answer 1

Okay, so I managed to somehow fix it after rebooting a million times (both soft reboot and hard reboot). Ran into a few mounting problems, ran into a few kernel panics, finally fixed all of the problems, but I don't know how/why. I would really like to know why everything was acting up so I can prevent it. So I'm going to detail everything that happened.
I decided I would like to game again, but not have to reboot into Windows. So to get a quick fix of my gaming dose, I decided to install a few games on Linux, and I added the gaming repo to my pacman.conf. I also wanted to use sage instead of excel, matlab, maple, and mathematica [and magma]. However, installing a few of my games and sage filled both /opt, /usr and /var to 100%. I was able to increase /opt and /usr easily because they were jfs. /var required me to go into my rescue cd. Then /usr ran out of space again, so I had to increase that again (/usr is now really fragmented, which I am not happy about). After I installed sage and most of the games I wanted, I decided to upgrade my system.
That's when I ran into the issue of removing '/usr/'. I tried a couple of times, hoping that it would fix itself, and then posted here. I installed a few more games without a problem, tried upgrading again with no success. Then I rebooted, Reboot process was fine. Still ran into the issue though. Tried upgrading again, and some packages upgraded partially (complained about not being able to write), most ran into the removing '/usr/' issue. I tried to startx, but ran into configuration errors, and I couldn't use my keyboard or mouse, so I hard rebooted.
Reboot went fine, I tried upgrading again. Pacman complained about files already existing, so I backed those up, and removed them. Tried upgrading again, kernel upgrade warned about not being mounted. So I tried to mount /boot, and it complained that ext2 was not a recognized filesystem. So I rebooted, ran into some module errors. I booted into the rescue CD, put back the modules I had backed up, and rebooted into the system. It booted up just fine. I upgraded, and it worked, except /boot still had trouble mounting. I booted into the rescue CD again, mounted the root filesystem into /mnt and the /boot partition into /blah, and copied the contents of /mnt/boot to /blah. Unfortunately, I forgot that would also override my grub configurations. So it ran into a kernel panic. After a few more reboots, I finally fixed the problem by replacing menu.lst with menu.lst~, and linking grub.conf to menu.lst. Now everything is working fine.
The issues I want to prevent from happening again is /usr mounted as read-write, but recognized as read-only, ext2 not being recognized (I can now mount /boot just fine). I would also like to know if it's possible that some of the packages weren't fully upgraded. If so, how can I get pacman to find them and re-install those packages.