System crash during yum update

***Gareth Jones*** · #1 11th July 2011, 01:43 AM

Hi all,

My system system suffers from frequent kernel panics, which I think are due to gnome-shell with the nVidia driver. (I see no panic message and nothing is logged, but I've enabled magic SysRq and it makes no difference.)

Twice this has occurred during yum-update's install stage, which is making me wonder.

yum-update then complained about an unfinished transaction, so I ran yum-complete-transaction as suggested. I've also tried yum-clean-all and rebuilding the RPM database, suggested in other threads, but I'm still seeing the following errors on yum-update:

--> Finished Dependency Resolution
Error: Protected multilib versions: 1:cups-libs-1.4.7-3.fc15.i686 != 1:cups-libs-1.4.6-15.fc15.x86_64
Error: Protected multilib versions: libuuid-2.19.1-1.3.fc15.i686 != libuuid-2.19.1-1.2.fc15.x86_64
Error: Protected multilib versions: krb5-libs-1.9.1-5.fc15.i686 != krb5-libs-1.9-7.fc15.x86_64
You could try using --skip-broken to work around the problem
** Found 23 pre-existing rpmdb problem(s), 'yum check' output follows:
1:NetworkManager-0.8.9997-5.git20110702.fc15.x86_64 is a duplicate with 1:NetworkManager-0.8.9997-4.git20110620.fc15.x86_64
1:NetworkManager-glib-0.8.9997-5.git20110702.fc15.x86_64 is a duplicate with 1:NetworkManager-glib-0.8.9997-4.git20110620.fc15.x86_64
1:cups-libs-1.4.7-3.fc15.x86_64 is a duplicate with 1:cups-libs-1.4.6-15.fc15.x86_64
ibus-1.3.99.20110419-9.fc15.x86_64 is a duplicate with ibus-1.3.99.20110419-7.fc15.x86_64

+ More errors of that ilk.

I don't know where these 32-bit packages have come from – this is an x86-64 system and the only x86-32 stuff I've intended to install is the Adobe flash plug-in. Also the later dupes are different 64-bit versions.

I've tried "package-cleanup --cleandupes" as suggested in this thread:
http://forums.fedoraforum.org/showth...tilib+versions
It wants to remove the old versions, but also wants to remove packages that depend on them, including clutter, so I cancelled that. The first time round I was left with a barely usable system and had to reinstall, which I'd rather avoid, especially if this is going to be a regular occurrence.

I'm not familiar with RPM (or kernel panics for that matter) – any suggestions would be appreciated!

Thanks,
Gareth

***Gareth Jones*** · #2 12th July 2011, 06:57 PM

Okay, given the lack of replies I decided to brave it and risk another hosed system. It was pretty epic. For reference, here's what I did to get back to a full up-to-date F15, in case anyone else finds themselves here.

'Complete' the interrupted YUM transaction:

Code:

sudo yum-complete-transaction

Get a list of currently installed packages:

Code:

sudo rpm -qa --qf '%{name} ' > ~/packages.old.txt

Remove the duplicate packages and update whatever is left:

Code:

sudo package-cleanup --cleandupes
sudo yum update

Get a new list of installed packages:

Code:

sudo rpm -qa --qf '%{name} ' > ~/packages.new.txt

Now I resorted to my old friend vim, but sed and sort would work too. I just like immediate interactive previews when dealing with regexes...

Open ~/packages.*.txt in vim. For each file break it into lines, sort and remove dupes. For the first line, "^M" is entered by pressing Ctrl+V, then Return.

Code:

:%s/ /^M/g
:sort u
:wq

Now compare the lists:

Code:

diff -u packages.{old,new}.txt > packages.diff

Open packages.diff in vim. Remove all lines except those starting with "-" (i.e. lost packages):

Code:

:%s/^ .*//
:%s/^+.*//
:%s/^---.*//
:%s/^%.*//

Remove the "-" prefixes and empty lines:

Code:

:%s/^-//
:sort u
:wq

Install the missing packages:

Code:

sudo yum install $(< ~/packages.diff)

Verify the installed RPMs:

Code:

sudo rpm -Va

Now I just need to know the best way to force a prelink run without confusing stuff...

Gareth