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Old 11-19-2011, 10:56 PM
Deron Meranda
 
Default System locked up during update of kernel, yum in unclean state and kernel half-installed

I ran the yum-complete-transaction but it seems to have refused to run
(output below).

# yum-complete-transaction
...
There are 1 outstanding transactions to complete. Finishing the most recent one
The remaining transaction had 10 elements left to run
--> Running transaction check
---> Package at.x86_64 0:3.1.13-3.fc16 will be erased
---> Package bind-libs.x86_64 32:9.8.1-2.fc16 will be erased
--> Processing Dependency: bind-libs = 32:9.8.1-2.fc16 for package:
32:bind-9.8.1-2.fc16.x86_64
---> Package bind-license.noarch 32:9.8.1-2.fc16 will be erased
---> Package facter.noarch 0:1.6.1-1.fc16 will be erased
---> Package kernel-headers.x86_64 0:3.1.1-1.fc16 will be erased
---> Package kernel-tools.x86_64 0:3.1.1-1.fc16 will be erased
---> Package nfs-utils.x86_64 1:1.2.5-1.fc16 will be erased
---> Package perl-IO-Socket-SSL.noarch 0:1.45-1.fc16 will be erased
---> Package setroubleshoot-plugins.noarch 0:3.0.14-2.fc15 will be erased
---> Package xfwm4.x86_64 0:4.8.1-5.fc16 will be erased
--> Running transaction check
---> Package bind.x86_64 32:9.8.1-2.fc16 will be erased
--> Finished Dependency Resolution

Dependencies Resolved

Transaction size changed - this means we are not doing the
same transaction as we were before. Aborting and disabling
this transaction.

You could try running: package-cleanup --problems
package-cleanup --dupes
rpm -Va --nofiles --nodigest

Transaction files renamed to:
/var/lib/yum/transaction-all.2011-11-19.16:27.59.disabled
/var/lib/yum/transaction-done.2011-11-19.16:27.59.disabled

***END***

# ls -l /var/lib/yum/transaction*
-rw-r--r--. 1 root root 1471 Nov 19 16:27
/var/lib/yum/transaction-all.2011-11-19.16:27.59.disabled
-rw-r--r--. 1 root root 1069 Nov 19 16:29
/var/lib/yum/transaction-done.2011-11-19.16:27.59.disabled


So I ran the package-cleanups it recommended:

# package-cleanup --problems
...
No Problems Found

# package-cleanup --dupes
...
perl-IO-Socket-SSL-1.45-1.fc16.noarch
perl-IO-Socket-SSL-1.49-1.fc16.noarch
bind-libs-9.8.1-4.P1.fc16.x86_64
bind-libs-9.8.1-2.fc16.x86_64
bind-9.8.1-2.fc16.x86_64
bind-9.8.1-4.P1.fc16.x86_64
nfs-utils-1.2.5-1.fc16.x86_64
nfs-utils-1.2.5-3.fc16.x86_64
facter-1.6.1-1.fc16.noarch
facter-1.6.2-1.fc16.noarch
setroubleshoot-plugins-3.0.17-1.fc16.noarch
setroubleshoot-plugins-3.0.14-2.fc15.noarch
at-3.1.13-3.fc16.x86_64
at-3.1.13-5.fc16.x86_64
bind-license-9.8.1-2.fc16.noarch
bind-license-9.8.1-4.P1.fc16.noarch
xfwm4-4.8.2-1.fc16.x86_64
xfwm4-4.8.1-5.fc16.x86_64


# yum check
...
at-3.1.13-5.fc16.x86_64 is a duplicate with at-3.1.13-3.fc16.x86_64
32:bind-9.8.1-4.P1.fc16.x86_64 is a duplicate with 32:bind-9.8.1-2.fc16.x86_64
32:bind-libs-9.8.1-4.P1.fc16.x86_64 is a duplicate with
32:bind-libs-9.8.1-2.fc16.x86_64
32:bind-license-9.8.1-4.P1.fc16.noarch is a duplicate with
32:bind-license-9.8.1-2.fc16.noarch
facter-1.6.2-1.fc16.noarch is a duplicate with facter-1.6.1-1.fc16.noarch
kernel-headers-3.1.1-2.fc16.x86_64 is a duplicate with
kernel-headers-3.1.1-1.fc16.x86_64
kernel-tools-3.1.1-2.fc16.x86_64 is a duplicate with
kernel-tools-3.1.1-1.fc16.x86_64
1:nfs-utils-1.2.5-3.fc16.x86_64 is a duplicate with
1:nfs-utils-1.2.5-1.fc16.x86_64
perl-IO-Socket-SSL-1.49-1.fc16.noarch is a duplicate with
perl-IO-Socket-SSL-1.45-1.fc16.noarch
setroubleshoot-plugins-3.0.17-1.fc16.noarch is a duplicate with
setroubleshoot-plugins-3.0.14-2.fc15.noarch
xfwm4-4.8.2-1.fc16.x86_64 is a duplicate with xfwm4-4.8.1-5.fc16.x86_64
Error: check all



Also my /boot still doesn't have the -2 kernel files installed.
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Old 11-19-2011, 11:45 PM
Deron Meranda
 
Default System locked up during update of kernel, yum in unclean state and kernel half-installed

I have run an rpm verify against all of the packages that were part of
the crashed yum update:

at-3.1.13-5.fc16.x86_64
bind-libs-9.8.1-4.P1.fc16.x86_64
bind-9.8.1-4.P1.fc16.x86_64
bind-license-9.8.1-4.P1.fc16.noarch
facter-1.6.2-1.fc16.noarch
kernel-3.1.1-2.fc16.x86_64
kernel-headers-3.1.1-2.fc16.x86_64
kernel-tools-3.1.1-2.fc16.x86_64
nfs-utils-1.2.5-3.fc16.x86_64
perl-IO-Socket-SSL-1.49-1.fc16.noarch
setroubleshoot-plugins-3.0.17-1.fc16.noarch
xfwm4-4.8.2-1.fc16.x86_64


Most of them show no discrepancies, except for "bind" and "kernel".
The one bind problem is just the ownership/permissions on the
/usr/lib64/bind/ directory.

But the kernel verify has lots of problems, all with size/MD5
mismatches. When I look at the individual files, almost all of them
are zero-length on my disk. I checked disk space, and there is plenty
of empty space in both / and /boot.


Even for the packages which verify fine, I still have two versions of
the packages installed (as reported by rpm -qi) - the previous
version and the new version. Obviously yum never got around to the
cleanup phase where it deleted the old versions.

How can I clean all this up? I tried just re-running the yum update
on the specific packages, but it complains, such as:

Error: Protected multilib versions: at-3.1.13-5.fc16.x86_64 !=
at-3.1.13-3.fc16.x86_64


Thanks again for any assistance.
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Old 11-20-2011, 12:14 AM
Kevin Fenzi
 
Default System locked up during update of kernel, yum in unclean state and kernel half-installed

On Sat, 19 Nov 2011 19:45:14 -0500
Deron Meranda <deron.meranda@gmail.com> wrote:

...snip...

> How can I clean all this up? I tried just re-running the yum update
> on the specific packages, but it complains, such as:
>
> Error: Protected multilib versions: at-3.1.13-5.fc16.x86_64 !=
> at-3.1.13-3.fc16.x86_64
>
>
> Thanks again for any assistance.

I'll suggest again:

yum history redo last

(or you may need to find out which tansaction it was with 'yum history
list' and then use that number instead of 'last')

kevin
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Old 11-20-2011, 12:36 AM
Deron Meranda
 
Default System locked up during update of kernel, yum in unclean state and kernel half-installed

> I'll suggest again:
>
> yum history redo last
>
> (or you may need to find out which tansaction it was with 'yum history
> list' and then use that number instead of 'last')


Thanks. I read right over that the first time.

Unfortunately it doesn't seem to have worked....

# yum history redo last
...
Repeating transaction 297, from Sat Nov 19 16:27:58 2011
** Updated at-3.1.13-3.fc16.x86_64 @anaconda-0
Update 3.1.13-5.fc16.x86_64 installed
Updated bind-32:9.8.1-2.fc16.x86_64 @anaconda-0
Update 32:9.8.1-4.P1.fc16.x86_64 installed
Updated bind-chroot-32:9.8.1-2.fc16.x86_64 @?fedora
Update 32:9.8.1-4.P1.fc16.x86_64 installed
** Updated bind-libs-32:9.8.1-2.fc16.x86_64 @anaconda-0
Update 32:9.8.1-4.P1.fc16.x86_64 installed
Updated bind-libs-lite-32:9.8.1-2.fc16.x86_64 @?fedora
Update 32:9.8.1-4.P1.fc16.x86_64 installed
** Updated bind-license-32:9.8.1-2.fc16.noarch @anaconda-0
Update 32:9.8.1-4.P1.fc16.noarch installed
Updated bind-utils-32:9.8.1-2.fc16.x86_64 @?fedora
Update 32:9.8.1-4.P1.fc16.x86_64 installed
** Updated facter-1.6.1-1.fc16.noarch @fedora
Update 1.6.2-1.fc16.noarch installed
Updated git-1.7.7.1-1.fc16.x86_64 @?_local
Update 1.7.7.3-1.fc16.x86_64 installed
Install kernel-3.1.1-2.fc16.x86_64 installed
Install kernel-devel-3.1.1-2.fc16.x86_64 installed
** Updated kernel-headers-3.1.1-1.fc16.x86_64 @updates
Update 3.1.1-2.fc16.x86_64 installed
** Updated kernel-tools-3.1.1-1.fc16.x86_64 @updates
Update 3.1.1-2.fc16.x86_64 installed
** Updated nfs-utils-1:1.2.5-1.fc16.x86_64 @anaconda-0
Update 1:1.2.5-3.fc16.x86_64 installed
Updated perl-Git-1.7.7.1-1.fc16.noarch @?_local
Update 1.7.7.3-1.fc16.noarch installed
** Updated perl-IO-Socket-SSL-1.45-1.fc16.noarch @anaconda-0
Update 1.49-1.fc16.noarch installed
Updated puppet-2.6.6-3.fc16.noarch @?fedora
Update 2.6.12-1.fc16.noarch installed
** Updated setroubleshoot-plugins-3.0.14-2.fc15.noarch
@anaconda-InstallationRepo-201105131943.x86_64/15
Update 3.0.17-1.fc16.noarch installed
** Updated xfwm4-4.8.1-5.fc16.x86_64 @anaconda-0
Update 4.8.2-1.fc16.x86_64 installed
Failed to upgrade: at-3.1.13-5.fc16.x86_64
Failed to upgrade: 32:bind-9.8.1-4.P1.fc16.x86_64
Failed to upgrade: 32:bind-chroot-9.8.1-4.P1.fc16.x86_64
Failed to upgrade: 32:bind-libs-9.8.1-4.P1.fc16.x86_64
Failed to upgrade: 32:bind-libs-lite-9.8.1-4.P1.fc16.x86_64
Failed to upgrade: 32:bind-license-9.8.1-4.P1.fc16.noarch
Failed to upgrade: 32:bind-utils-9.8.1-4.P1.fc16.x86_64
Failed to upgrade: facter-1.6.2-1.fc16.noarch
Failed to upgrade: git-1.7.7.3-1.fc16.x86_64
Failed to upgrade: kernel-headers-3.1.1-2.fc16.x86_64
Failed to upgrade: kernel-tools-3.1.1-2.fc16.x86_64
Failed to upgrade: 1:nfs-utils-1.2.5-3.fc16.x86_64
Failed to upgrade: perl-Git-1.7.7.3-1.fc16.noarch
Failed to upgrade: perl-IO-Socket-SSL-1.49-1.fc16.noarch
Failed to upgrade: puppet-2.6.12-1.fc16.noarch
Failed to upgrade: setroubleshoot-plugins-3.0.17-1.fc16.noarch
Failed to upgrade: xfwm4-4.8.2-1.fc16.x86_64
Package kernel-3.1.1-2.fc16.x86_64 already installed and latest version
Package kernel-devel-3.1.1-2.fc16.x86_64 already installed and latest version
history redo


And then doing a "yum check" again confirms that it is still confused
and has multiple versions installed.

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Old 11-20-2011, 01:05 AM
Tom Horsley
 
Default System locked up during update of kernel, yum in unclean state and kernel half-installed

On Sat, 19 Nov 2011 20:36:47 -0500
Deron Meranda wrote:

> And then doing a "yum check" again confirms that it is still confused
> and has multiple versions installed.

The last time I got in this state, I finally resorted to
doing low-level rpm commands to remove the old versions of
the duplicates,but used the options to avoid running
scripts and triggers and also the all-important --nodeps
so it wouldn't screw up even more packages.

Then, while the system was still up after doing that,
I did a yum reinstall of all of those packages without
specifying a particular version to get
the updates installed for sure, and I think
my system was happy after that (at least I haven't yet run
into any problems).
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Old 11-20-2011, 02:24 AM
Kevin Fenzi
 
Default System locked up during update of kernel, yum in unclean state and kernel half-installed

On Sat, 19 Nov 2011 20:36:47 -0500
Deron Meranda <deron.meranda@gmail.com> wrote:

> > I'll suggest again:
> >
> > yum history redo last
> >
> > (or you may need to find out which tansaction it was with 'yum
> > history list' and then use that number instead of 'last')
>
>
> Thanks. I read right over that the first time.
>
> Unfortunately it doesn't seem to have worked....

...snip...

> And then doing a "yum check" again confirms that it is still confused
> and has multiple versions installed.

ok. Then I fear you will need to go to:

package-cleanup --cleandupes

kevin


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Old 11-20-2011, 04:22 AM
Deron Meranda
 
Default System locked up during update of kernel, yum in unclean state and kernel half-installed

Kevin Fenzi said:
> ok. Then I fear you will need to go to:
>
> package-cleanup --cleandupes


Great news. I think I've finally got my system back to a clean and
updated state! Thanks everybody who helped. I only have one curious
error message about a missing grubby template (explained toward the
end).


For everybody's benefit, here's what I did...

The first thing I did was to create an LVM snapshot for both my / and
/var logical volumes; just in case. I actually should have done that
at the beginning of the whole initial "yum update", and it would have
been way easier to back out.

Then I ran "package-cleanup --cleandupes" as suggested. This removed
all the duplicate packages (the older versions of each) for all the
packages, except the kernel packages. This was expected I guess
because yum by default will keep multiple versions of the kernel
installed; which is a good thing!

At that point I re-verified all the other packages, except the kernel,
using rpm --verify. And also did a "yum check", which now only
complains about the kernel. I also verified the previous version of
the kernel, just to insure myself that it was still okay.

Now I already know the latest kernel did not get installed properly as
there are lots of zero-length files, etc. So I manually uninstalled it
(knowing my previous kernel version was intact).

rpm -e kernel-tools-3.1.1-2.fc16.x86_64
kernel-headers-3.1.1-2.fc16.x86_64
kernel-devel-3.1.1-2.fc16.x86_
64 kernel-3.1.1-2.fc16.x86_64

At this point yum check is all happy! And there is no trace of the
3.1.1-2 version of kernel packages in the rpm database.

So I at this point tried a plain old "yum update" again.

It correctly identified that I needed to update the kernel packages
(kernel, kernel-devel, kernel-header, kernel-tools). I let it proceed,
and eventually it completed and now I have the system updated. And the
new kernel verifies ok!


Note, there was ONE ERROR/WARNING message I saw during the install
about a missing grubby template which I still need to investigate.
Here's the yum update output...

Running Transaction
Warning: RPMDB altered outside of yum.
Updating : kernel-headers-3.1.1-2.fc16.x86_64
1/6
Installing : kernel-devel-3.1.1-2.fc16.x86_64
2/6
Updating : kernel-tools-3.1.1-2.fc16.x86_64
3/6
Installing : kernel-3.1.1-2.fc16.x86_64
4/6
grubby fatal error: unable to find a suitable template
Cleanup : kernel-headers-3.1.1-1.fc16.x86_64
5/6
Cleanup : kernel-tools-3.1.1-1.fc16.x86_64
6/6
yum-updatesd not on the bus

Installed:
kernel.x86_64 0:3.1.1-2.fc16
kernel-devel.x86_64 0:3.1.1-2.fc16

Updated:
kernel-headers.x86_64 0:3.1.1-2.fc16
kernel-tools.x86_64 0:3.1.1-2.fc16



My next step is to reboot into the new kernel. And once I'm sure
everything is fine, I can remove those LVM snapshots.



Thanks again everybody. Oh, any idea about the grubby error?
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Old 11-20-2011, 04:32 AM
Sam Varshavchik
 
Default System locked up during update of kernel, yum in unclean state and kernel half-installed

Deron Meranda writes:


Thanks again everybody. Oh, any idea about the grubby error?


Did you update from F15?

You probably have /etc/grub.cfg and /boot/grub left lying around. That
confuses grubby. You can remove /etc/grub.cfg to shut it up, then, in a few
months, once the confidence level in grub2 comes up, nuke everything in
/boot/grub.


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Old 11-20-2011, 04:50 AM
Deron Meranda
 
Default System locked up during update of kernel, yum in unclean state and kernel half-installed

>> Thanks again everybody. *Oh, any idea about the grubby error?
>
> Did you update from F15?
>
> You probably have /etc/grub.cfg and /boot/grub left lying around. That
> confuses grubby. You can remove /etc/grub.cfg to shut it up, then, in a few
> /boot/grub.


Yes, it was an upgrade from F15, which was an upgrade from F14,
....etc.... And yes, the old grub stuff is still lying around, I was
wondering about that a bit.


One more interesting thing... I just completed my reboot, and my
system now seems quite happy.
However when I selected the kernel to use in the grub menu, it quickly said

Loading Fedora (3.1.1-1.fc16.x86_64)

even though I had explicitly selected the -2 revision, not the -1.
However once the kernel
got control and output its own version it did say -2. And likewise
/proc/version confirms
as well that I'm running on the -2 revision.

So I poked around and found this in my /boot/grub2/grub.cfg file...

menuentry 'Fedora (3.1.1-2.fc16.x86_64)' --class fedora --class
gnu-linux --class gnu --class os {
load_video
set gfxpayload=keep
insmod gzio
insmod part_msdos
insmod ext2
set root='(hd0,msdos1)'
search --no-floppy --fs-uuid --set=root
b9b2e74c-1e4f-49ef-a4b1-687f7a58fa14
echo 'Loading Fedora (3.1.1-1.fc16.x86_64)'
linux /vmlinuz-3.1.1-2.fc16.x86_64
root=/dev/mapper/vg_beryl-lvroot ro rd.md=0 rd.dm=0
rd.lvm.lv=vg_beryl/lvroot KEYT
ABLE=us quiet SYSFONT=latarcyrheb-sun16 rhgb rd.luks=0 LANG=en_US.UTF-8
echo 'Loading initial ramdisk ...'
initrd /initramfs-3.1.1-2.fc16.x86_64.img
}


Notice how the "echo" line has the wrong version number, while
everything else is right!


Is anybody else seeing that? I just want to know if it is somehow
still an artifact of the yum upgrade mess I had gotten into?

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Old 11-20-2011, 01:44 PM
"T.C. Hollingsworth"
 
Default System locked up during update of kernel, yum in unclean state and kernel half-installed

On Sat, Nov 19, 2011 at 10:50 PM, Deron Meranda <deron.meranda@gmail.com> wrote:
> One more interesting thing... I just completed my reboot, and my
> system now seems quite happy.
> However when I selected the kernel to use in the grub menu, it quickly said
>
> * Loading Fedora (3.1.1-1.fc16.x86_64)
>
> even though I had explicitly selected the -2 revision, not the -1.
> However once the kernel
> got control and output its own version it did say -2. And likewise
> /proc/version confirms
> as well that I'm running on the -2 revision.
>
> So I poked around and found this in my /boot/grub2/grub.cfg file...
>
> menuentry 'Fedora (3.1.1-2.fc16.x86_64)' --class fedora --class
> gnu-linux --class gnu --class os {
> * * * *load_video
> * * * *set gfxpayload=keep
> * * * *insmod gzio
> * * * *insmod part_msdos
> * * * *insmod ext2
> * * * *set root='(hd0,msdos1)'
> * * * *search --no-floppy --fs-uuid --set=root
> b9b2e74c-1e4f-49ef-a4b1-687f7a58fa14
> * * * *echo 'Loading Fedora (3.1.1-1.fc16.x86_64)'
> * * * *linux * /vmlinuz-3.1.1-2.fc16.x86_64
> root=/dev/mapper/vg_beryl-lvroot ro rd.md=0 rd.dm=0
> rd.lvm.lv=vg_beryl/lvroot *KEYT
> ABLE=us quiet SYSFONT=latarcyrheb-sun16 rhgb rd.luks=0 LANG=en_US.UTF-8
> * * * *echo 'Loading initial ramdisk ...'
> * * * *initrd /initramfs-3.1.1-2.fc16.x86_64.img
> }
>
>
> Notice how the "echo" line has the wrong version number, while
> everything else is right!
>
>
> Is anybody else seeing that? *I just want to know if it is somehow
> still an artifact of the yum upgrade mess I had gotten into?

This is a known bug that affects even fresh installations:
https://bugzilla.redhat.com/show_bug.cgi?id=732654

It's completely harmless.

-T.C.
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