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Old 12-15-2007, 11:52 PM
Joe Smith
 
Default yum updates corrupting rpmdb

This is the second update in as many days that has resulted in a
corrupted rpm database for me. I was able to fix yesterday's with a
--rebuilddb and 'yum clean all' but before I go through that little
exercise again, is anyone else seeing problems? Any suggestions how to
debug this?


# yum update
( lists a dozen or so packages to update, including firefox...
...I say 'y'...
...10 minutes later the terminal history is filled with:
rpmdb: PANIC: fatal region error detected; run recovery
rpmdb: PANIC: fatal region error detected; run recovery

and yum won't die except by 'kill -9'

# rpm -qa
rpmdb: PANIC: fatal region error detected; run recovery
error: db4 error(-30977) from dbenv->open: DB_RUNRECOVERY: Fatal error,
run database recovery

error: cannot open Packages index using db3 - (-30977)
error: cannot open Packages database in /var/lib/rpm

Not out of space...
# df /var/lib/rpm
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/sdb7 497829 205804 266323 44% /var

and there are no kernel disk error messages.

Is there some "run recovery" that's different than --rebuilddb?

<Joe

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Old 12-16-2007, 12:15 AM
Craig White
 
Default yum updates corrupting rpmdb

On Sat, 2007-12-15 at 19:52 -0500, Joe Smith wrote:
> This is the second update in as many days that has resulted in a
> corrupted rpm database for me. I was able to fix yesterday's with a
> --rebuilddb and 'yum clean all' but before I go through that little
> exercise again, is anyone else seeing problems? Any suggestions how to
> debug this?
>
> # yum update
> ( lists a dozen or so packages to update, including firefox...
> ...I say 'y'...
> ...10 minutes later the terminal history is filled with:
> rpmdb: PANIC: fatal region error detected; run recovery
> rpmdb: PANIC: fatal region error detected; run recovery
>
> and yum won't die except by 'kill -9'
>
> # rpm -qa
> rpmdb: PANIC: fatal region error detected; run recovery
> error: db4 error(-30977) from dbenv->open: DB_RUNRECOVERY: Fatal error,
> run database recovery
> error: cannot open Packages index using db3 - (-30977)
> error: cannot open Packages database in /var/lib/rpm
>
> Not out of space...
> # df /var/lib/rpm
> Filesystem 1K-blocks Used Available Use% Mounted on
> /dev/sdb7 497829 205804 266323 44% /var
>
> and there are no kernel disk error messages.
>
> Is there some "run recovery" that's different than --rebuilddb?
----
no but perhaps your /dev/sdb7 has some corruption itself.

You might try something like 'shutdown now -Fr' to force an fsck on
reboot

Craig

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Old 12-16-2007, 03:54 AM
Joe Smith
 
Default yum updates corrupting rpmdb

Craig White wrote:

...

Is there some "run recovery" that's different than --rebuilddb?

----
no but perhaps your /dev/sdb7 has some corruption itself.

You might try something like 'shutdown now -Fr' to force an fsck on
reboot


Thanks for the suggestion, but no, it checks clean. Badblocks comes up
clean also.


I tried dropping to single user to run fsck, but couldn't unmount /var.
There were no open files on it, so maybe it's connected to whatever was
preventing yum from being killed; maybe a database block was locked or
something, I don't know.


It could be last time, because I rebuilt the database before I rebooted,
there was still this strange problem with the partition, so maybe the
database still was not clean.


So, I rebooted to single-user; rpm --rebuilddb; yum clean all

Now rpm is working again, but yum reports no updates are available, even
though there are packages announced for updates that should apply to me:


# yum list firefox gnome-python2, ...
Installed Packages
autofs.i386 1:5.0.2-17 installed
firefox.i386 2.0.0.10-2.fc8 installed
gnome-python2.i386 2.20.0-1.fc8 installed
lftp.i386 3.5.14-2.fc8 installed
libshout.i386 2.2.2-1.fc6 installed
libsoup.i386 2.2.103-1.fc8 installed
nspluginwrapper.i386 0.9.91.5-12.fc8 installed
system-config-firewall.noarch 1.0.11-1.fc8 installed

Yet, todays update annoucements list:

[SECURITY] Fedora 8 Update: autofs-5.0.2-20 updates
Fedora 8 Update: firefox-2.0.0.10-3.fc8 updates
Fedora 8 Update: gnome-python2-2.20.1-1.fc8 updates
Fedora 8 Update: lftp-3.5.14-3.fc8 updates
Fedora 8 Update: libshout-2.2.2-2.fc8 updates
Fedora 8 Update: libsoup-2.2.104-1.fc8 updates
Fedora 8 Update: nspluginwrapper-0.9.91.5-13.fc8 updates
Fedora 8 Update: system-config-firewall-1.0.12-2.fc8 updates

So it looks like all these packages should be upgraded, but yum says no.

I remember at least a few of those being in the update list before yum
went berserk, so something sure looks off-track here.


What could cause that? Maybe the updates have not reached the mirrors
yet? Surely yum doesn't depend on that to determine what upgrades are
available.


Hmm... out of desperation, I ran another "yum clean all" and now it's
picking up all those updates. So I wasn't crazy--yum was just fouled up
again.


Suggestions welcome--let's see if I can actually do the updates this
time. Two down, five left.


<Joe

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Old 12-16-2007, 11:40 AM
Craig White
 
Default yum updates corrupting rpmdb

On Sat, 2007-12-15 at 23:54 -0500, Joe Smith wrote:
> Craig White wrote:
> > ...
> >> Is there some "run recovery" that's different than --rebuilddb?
> > ----
> > no but perhaps your /dev/sdb7 has some corruption itself.
> >
> > You might try something like 'shutdown now -Fr' to force an fsck on
> > reboot
>
> Thanks for the suggestion, but no, it checks clean. Badblocks comes up
> clean also.
>
> I tried dropping to single user to run fsck, but couldn't unmount /var.
> There were no open files on it, so maybe it's connected to whatever was
> preventing yum from being killed; maybe a database block was locked or
> something, I don't know.
>
> It could be last time, because I rebuilt the database before I rebooted,
> there was still this strange problem with the partition, so maybe the
> database still was not clean.
>
> So, I rebooted to single-user; rpm --rebuilddb; yum clean all
>
> Now rpm is working again, but yum reports no updates are available, even
> though there are packages announced for updates that should apply to me:
>
> # yum list firefox gnome-python2, ...
> Installed Packages
> autofs.i386 1:5.0.2-17 installed
> firefox.i386 2.0.0.10-2.fc8 installed
> gnome-python2.i386 2.20.0-1.fc8 installed
> lftp.i386 3.5.14-2.fc8 installed
> libshout.i386 2.2.2-1.fc6 installed
> libsoup.i386 2.2.103-1.fc8 installed
> nspluginwrapper.i386 0.9.91.5-12.fc8 installed
> system-config-firewall.noarch 1.0.11-1.fc8 installed
>
> Yet, todays update annoucements list:
>
> [SECURITY] Fedora 8 Update: autofs-5.0.2-20 updates
> Fedora 8 Update: firefox-2.0.0.10-3.fc8 updates
> Fedora 8 Update: gnome-python2-2.20.1-1.fc8 updates
> Fedora 8 Update: lftp-3.5.14-3.fc8 updates
> Fedora 8 Update: libshout-2.2.2-2.fc8 updates
> Fedora 8 Update: libsoup-2.2.104-1.fc8 updates
> Fedora 8 Update: nspluginwrapper-0.9.91.5-13.fc8 updates
> Fedora 8 Update: system-config-firewall-1.0.12-2.fc8 updates
>
> So it looks like all these packages should be upgraded, but yum says no.
>
> I remember at least a few of those being in the update list before yum
> went berserk, so something sure looks off-track here.
>
> What could cause that? Maybe the updates have not reached the mirrors
> yet? Surely yum doesn't depend on that to determine what upgrades are
> available.
>
> Hmm... out of desperation, I ran another "yum clean all" and now it's
> picking up all those updates. So I wasn't crazy--yum was just fouled up
> again.
>
> Suggestions welcome--let's see if I can actually do the updates this
> time. Two down, five left.
----
did you want some cheese with that whine?

man yum.conf

metadata_expire
Time (in seconds) after which the metadata will expire. So that if the
current metadata downloaded is less than this many seconds old then yum
will not update the metadata against the repository. If you find that
yum is not downloading information on updates as often as you would like
lower the value of this option.

Craig

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