yum - Error: database disk image is malformed

If you've ever gotten this cryptic error using yum, you'll find that it's very difficult to pinpoint the cause. The message itself, "database disk image is malformed," refers to a corrupted sqlite file. However, the RPM and YUM systems use a variety of different such files; therefore finding the right one can be difficult.

The best thing to do, is to start by attempting to fix this using the available command line tool:

# yum clean all

This should solve the problem in most cases.  If the problem continues, perhaps the RPM database files are corrupted. One of my previous articles talks about rebuilding these, but I will go over it again here:

The database files are located in "/var/lib/rpm" and are named __db.001 __db.002 etc... etc...

Delete those files:

# rm -f /var/lib/rpm/__db*

Rebuild the database:

# rpm --rebuilddb

Then try to clean the yum cache as per the above command and try your yum command again.  If this continues to fail, try deleting your yum cache manually:

# rm -Rf /var/cache/yum

Now try the command again.  This should have gotten rid of the last sqlite files yum could possibly use.  The command should be able to rebuild all the databases correctly at this point.

yum crashed with python import error - fixed corrupted rpm database

I ran into an interesting error while trying to find out, which repository one of my installed packages came from.  Before we proceed, let me explain that I had need to use the "repoquery" utility which is part of the "yum-utils" package.  I proceeded to install this one as I did not yet have it.  The installation worked perfectly well and did not install any dependencies.

# yum install yum-utils -y

Using the repoquery command, I attempted to query which repo my php53 package came from:

$ repoquery -i php53

Instead of getting the information I wanted, the script crashed with the following error:

File "/usr/bin/repoquery", line 38, in

from yum.i18n import to_unicode

cannot import name to_unicode

Googling around, many blog posts and site talked about the yum installation being broken.  That may well be, but I decided to see if maybe there was something a bit simpler at play here.  First I needed to find out which yum packages are already installed on this system:

# rpm -qa | grep -i yum

yum-fastestmirror-1.1.16-16.el5.centos
yum-3.2.22-37.el5.centos
yum-updatesd-0.9-2.el5
yum-utils-1.1.16-16.el5.centos
yum-metadata-parser-1.1.2-2.el5

NOTE: The listed version numbers do not reflect the original numbers I had on my system.  I went ahead and attempted to update all of the above listed packages:

# yum update yum yum-fastestmirror yum-updatesd yum-metadata-parser

Yum only found that yum and yum-fastestmirror needed to be updated.  I proceeded with the update.

After the update, the repoquery command started working perfectly well.  However, a completely unrelated problem occurred which I will discuss very briefly.

# repoquery -i php53

Instead of getting a nice listing of information from the RPM database, I received an error message saying the database was corrupted.  The next step then was to rebuild the dabase.  

The database files are located in "/var/lib/rpm" and are named __db.001 __db.002 etc... etc...

Delete those files:

# rm -f /var/lib/rpm/__db*

Rebuild the database:

# rpm -vv --rebuilddb

Once completed, I tried the repoquery command once again:

# repoquery -i php53

Name        : php53
Version     : 5.3.3
Release     : 1.el5_7.6
Architecture: x86_64
Size        : 3591477
Packager    : None
Group       : Development/Languages
URL         : http://www.php.net/
Repository  : updates
Summary     : PHP scripting language for creating dynamic web sites
Description :
PHP is an HTML-embedded scripting language. PHP attempts to make it
easy for developers to write dynamically generated webpages. PHP also
offers built-in database integration for several commercial and
non-commercial database management systems, so writing a
database-enabled webpage with PHP is fairly simple. The most common
use of PHP coding is probably as a replacement for CGI scripts.

The php package contains the module which adds support for the PHP
language to Apache HTTP Server.

Cannot remove package with yum due to corruption

During an attempt to reinstall some packages with yum today, I ran into an unexpected issue.  Yum responded with the following error, when I was trying to reinstall NetworkManager:

Error in PREUN scriptlet in rpm package NetworkManager
1:NetworkManager-0.8.3.997-1.fc14.x86_64 was supposed to be removed but is not!

When this happens you will need to remove the RPM package manually.  However, since an error occurred in the rpm's pre and post install scripts, you will need to disable it by specifying the --noscript option.

Note that this should be a last resort and can be dangerous.  Rpm.org explains this in more details:
http://www.rpm.org/max-rpm/s1-rpm-install-additional-options.html#S2-RPM-INSTALL-NOSCRIPTS

In my particular case I successfully reinstalled NetworkManager after removing it with the following command:

$ sudo rpm -e --noscripts