[SOLVED] yum failed: unexpected file type or format

[daytooner]

Running 64 bit F16. Trying to do an update via yum, and got this:

error: rpmdb: __db_meta_setup: /var/lib/rpm/Obsoletename: unexpected file type or format
... repeated many times ...
ERROR with transaction check vs depsolve:
libclutter-gtk-0.10.so.0()(64bit) is needed by gthumb-2.14.4-1.fc16.x86_64
Please report this error in https://bugzilla.redhat.com/enter_bu...&component=yum
** Found 1 pre-existing rpmdb problem(s), 'yum check' output follows:
gthumb-2.14.3-1.fc16.x86_64 has missing requires of libclutter-gtk-0.10.so.0()(64bit)

I get a similar error even when I try to install a package. Also, I couldn't even upgrade to F17 - I get a similar failure.

What's going on here? Can this be fixed? Or do I need to reinstall my OS from scratch? I had problems with yum on F15, which made me do a fresh installation (so I went with F16 then).

This is getting frustrating. Please help.

TIA

ken

[mschwendt]

Make a backup of all files in /var/lib/rpm/.

Try to rebuild the RPM DB: rpm -vv --rebuilddb

Run yum check and then try to install missing packages to fix any broken dependencies. For example: yum install 'libclutter-gtk-0.10.so.0()(64bit)'

If trying to install something fails, run yum or repoquery to verify whether the needed thing is available. You can also try to use "yum reinstall …" to try to reinstall a package.

[daytooner]

Originally Posted by mschwendt

Make a backup of all files in /var/lib/rpm/.

Try to rebuild the RPM DB: rpm -vv --rebuilddb

Run yum check and then try to install missing packages to fix any broken dependencies. For example: yum install 'libclutter-gtk-0.10.so.0()(64bit)'

If trying to install something fails, run yum or repoquery to verify whether the needed thing is available. You can also try to use "yum reinstall …" to try to reinstall a package.

Tried rebuilding rpm db, even cleaning out all of yum's data. But the problem still exists.

I read somewhere (while googling for this) about a problem with an upgrade to rpm, something about a new database format(?). Nothing was very clear. Also checked bugzilla, but didn't find anything. Did post a bug, but haven't heard back.

BTW: seems I'm not the only one with this problem: http://forums.fedoraforum.org/showthread.php?t=281997

Thx,

ken

[mschwendt]

You haven't tried to install the missing package(s), have you? The yum install command I've mentioned.

So, I've done some searching for you (as I'm mostly on F17 and F18 and no longer on F16):

libclutter-gtk-0.10.so.0()(64bit) is needed by gthumb-2.14.4-1.fc16.x86_64
gthumb-2.14.3-1.fc16.x86_64 has missing requires of libclutter-gtk-0.10.so.0()(64bit)

This is the latest gthumb for F16:
https://admin.fedoraproject.org/upda...-2.14.4-1.fc16

It requires libclutter-gtk-0.10.so.0()(64bit) which is provided by the clutter-gtk010 package:
https://admin.fedoraproject.org/upda...-0.10.8-5.fc16

yum install clutter-gtk010 would also install it.

[daytooner]

Originally Posted by mschwendt

You haven't tried to install the missing package(s), have you? The yum install command I've mentioned.

So, I've done some searching for you (as I'm mostly on F17 and F18 and no longer on F16):


This is the latest gthumb for F16:
https://admin.fedoraproject.org/upda...-2.14.4-1.fc16

It requires libclutter-gtk-0.10.so.0()(64bit) which is provided by the clutter-gtk010 package:
https://admin.fedoraproject.org/upda...-0.10.8-5.fc16

yum install clutter-gtk010 would also install it.

The problem seems to be more than just a missing dependency:

[root@Foghorn ~]# yum install clutter-gtk010
Loaded plugins: langpacks, presto, refresh-packagekit
Resolving Dependencies
--> Running transaction check
---> Package clutter-gtk010.x86_64 0:0.10.8-5.fc16 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

================================================== ==============================
Package Arch Version Repository Size
================================================== ==============================
Installing:
clutter-gtk010 x86_64 0.10.8-5.fc16 fedora 42 k

Transaction Summary
================================================== ==============================
Install 1 Package

Total download size: 42 k
Installed size: 42 k
Is this ok [y/N]: y
Downloading Packages:
clutter-gtk010-0.10.8-5.fc16.x86_64.rpm | 42 kB 00:02
Running Transaction Check
error: rpmdb: __db_meta_setup: /var/lib/rpm/Obsoletename: unexpected file type or format
error: cannot open Obsoletename index using db4 - Invalid argument (22)
Running Transaction Test
Transaction Test Succeeded
Running Transaction
Traceback (most recent call last):
File "/bin/yum", line 29, in <module>
yummain.user_main(sys.argv[1:], exit_code=True)
File "/usr/share/yum-cli/yummain.py", line 321, in user_main
errcode = main(args)
File "/usr/share/yum-cli/yummain.py", line 229, in main
return_code = base.doTransaction()
File "/usr/share/yum-cli/cli.py", line 646, in doTransaction
resultobject = self.runTransaction(cb=cb)
File "/usr/lib/python2.7/site-packages/yum/__init__.py", line 1613, in runTransaction
lastdbv = self.history.last()
File "/usr/lib/python2.7/site-packages/yum/history.py", line 1265, in last
ret = self.old([], 1, complete_transactions_only)
File "/usr/lib/python2.7/site-packages/yum/history.py", line 1214, in old
executeSQL(cur, sql, params)
File "/usr/lib/python2.7/site-packages/yum/sqlutils.py", line 166, in executeSQLQmark
return cursor.execute(query)
sqlite3.DatabaseError: database disk image is malformed
[root@Foghorn ~]#

Also note:

[root@Foghorn ~]# yum erase preupgrade
Loaded plugins: langpacks, presto, refresh-packagekit
Resolving Dependencies
--> Running transaction check
---> Package preupgrade.noarch 0:1.1.10-1.fc16 will be erased
--> Finished Dependency Resolution

Dependencies Resolved

================================================================================
 Package           Arch          Version               Repository          Size
================================================================================
Removing:
 preupgrade        noarch        1.1.10-1.fc16         @anaconda-0        772 k

Transaction Summary
================================================================================
Remove  1 Package

Installed size: 772 k
Is this ok [y/N]: y
Downloading Packages:
Running Transaction Check
Running Transaction Test
Transaction Test Succeeded
Running Transaction
Traceback (most recent call last):
  File "/bin/yum", line 29, in <module>
    yummain.user_main(sys.argv[1:], exit_code=True)
  File "/usr/share/yum-cli/yummain.py", line 321, in user_main
    errcode = main(args)
  File "/usr/share/yum-cli/yummain.py", line 229, in main
    return_code = base.doTransaction()
  File "/usr/share/yum-cli/cli.py", line 646, in doTransaction
    resultobject = self.runTransaction(cb=cb)
  File "/usr/lib/python2.7/site-packages/yum/__init__.py", line 1613, in runTransaction
    lastdbv = self.history.last()
  File "/usr/lib/python2.7/site-packages/yum/history.py", line 1265, in last
    ret = self.old([], 1, complete_transactions_only)
  File "/usr/lib/python2.7/site-packages/yum/history.py", line 1214, in old
    executeSQL(cur, sql, params)
  File "/usr/lib/python2.7/site-packages/yum/sqlutils.py", line 166, in executeSQLQmark
    return cursor.execute(query)
sqlite3.DatabaseError: database disk image is malformed
[root@Foghorn ~]#

I had a similar problem in F15, and I couldn't get the database de-corrupted. So I ended up re-installing F15, and then, soon after, upgrading to F16 via preupgrade. That seemed to work for a while, until some package got updated which corrupted the database again.

Since nothing seems to fix this, I'll probably just install a fresh F17. Fortunately all of my data is on a network drive, so the only things I'm losing are my configuration settings, and the time it takes to install and reconfigure everything.

Any other suggestions still appreciated.

Thx,

ken

---------- Post added at 07:12 PM ---------- Previous post was at 05:11 PM ----------

Holy repos Batman!

After doing some more googling, I found another thread about the same problem. The final solution was to try:

yum history new

And, wow, it works now!

KISS.

Thx for the help.

ken

[mschwendt]

Well, you didn't tell whether "rpm --rebuilddb" failed with the same error. Normally, it recreates the /var/lib/rpm/Obsoletename file, but if it fails trying to read it, you would need to delete it first, then rebuild the RPM DB.

About "yum history new" and the other sqlite3 error, that's completely unrelated from your earlier errors and does not touch the RPM DB. Yum history is related to files in /var/lib/yum/history, so flushing the history cannot fix the other errors.

[daytooner]

Originally Posted by mschwendt

Well, you didn't tell whether "rpm --rebuilddb" failed with the same error. Normally, it recreates the /var/lib/rpm/Obsoletename file, but if it fails trying to read it, you would need to delete it first, then rebuild the RPM DB.

About "yum history new" and the other sqlite3 error, that's completely unrelated from your earlier errors and does not touch the RPM DB. Yum history is related to files in /var/lib/yum/history, so flushing the history cannot fix the other errors.

"rpm --rebuilddb" didn't fail. But when I ran "yum update" after that, I got the same errors.

Not knowing the internals of yum or rpm (and not really wanting to), I have NO idea why, but "yum history new" did fix the problem. The update then proceeded and finished successfully.

ken

[mschwendt]

That's because only later you've shown the other error. Your initial quote does not refer to any sqlite3 error.