7/22/2014 How To Fix "Error: database disk image is malformed" On CentOS / Fedora | Unixmen

How To Fix “Error: database disk

image is malformed” On CentOS /
Fedora
by SK

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Today I have been trying to update my CentOS 6.5 virtual machine using command “yum update”.

# yum update

Sample output:

Loaded plugins: fastestmirror, security

Loading mirror speeds from cached hostfile
* base: centos.aol.in
* epel: epel.mirror.net.in
* extras: centos.aol.in
* remi: mirror.smartmedia.net.id
* remi-php55: mirror.smartmedia.net.id
* rpmforge: mirrors.ispros.com.bd
* rpmfusion-free-updates: mirror.smartmedia.net.id
* rpmfusion-nonfree-updates: mirror.smartmedia.net.id
* updates: centos.aol.in
Error: database disk image is malformed

I got a weird error “Error: database disk image is malformed”and my system didn’t get updated.

How do I solve this error?

It was very simple. After a couple of hours hunting for a solution, I got a working solution from
Fedora Forums.

To get rid of this above error, enter the following command From Terminal:

# yum clean dbcache

Then I tried again to update the system with the command:

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# yum update

Sample output:

Loaded plugins: fastestmirror, security

Loading mirror speeds from cached hostfile
* base: centos.aol.in
* epel: epel.mirror.net.in
* extras: centos.aol.in
* remi: mirror.smartmedia.net.id
* remi-php55: mirror.smartmedia.net.id
* rpmforge: mirrors.ispros.com.bd
* rpmfusion-free-updates: mirror.smartmedia.net.id
* rpmfusion-nonfree-updates: mirror.smartmedia.net.id
* updates: centos.aol.in
Setting up Update Process
Resolving Dependencies
--> Running transaction check
---> Package bind-libs.i686 32:9.8.2-0.17.rc1.el6_4.6 will be updated
---> Package bind-libs.i686 32:9.8.2-0.23.rc1.el6_5.1 will be an update
---> Package bind-utils.i686 32:9.8.2-0.17.rc1.el6_4.6 will be updated
---> Package bind-utils.i686 32:9.8.2-0.23.rc1.el6_5.1 will be an update
---> Package irqbalance.i686 2:1.0.4-6.el6 will be updated
---> Package irqbalance.i686 2:1.0.4-8.el6_5 will be an update
---> Package java-1.6.0-openjdk.i686 1:1.6.0.0-1.66.1.13.0.el6 will be updated
---> Package java-1.6.0-openjdk.i686 1:1.6.0.0-3.1.13.1.el6_5 will be an update
---> Package java-1.7.0-openjdk.i686 1:1.7.0.45-2.4.3.4.el6_5 will be updated
---> Package java-1.7.0-openjdk.i686 1:1.7.0.51-2.4.4.1.el6_5 will be an update
---> Package kernel.i686 0:2.6.32-431.5.1.el6 will be installed
---> Package kernel-firmware.noarch 0:2.6.32-431.3.1.el6 will be updated
---> Package kernel-firmware.noarch 0:2.6.32-431.5.1.el6 will be an update
---> Package kernel-headers.i686 0:2.6.32-431.3.1.el6 will be updated
---> Package kernel-headers.i686 0:2.6.32-431.5.1.el6 will be an update
---> Package mysql.i686 0:5.5.35-1.el6.remi will be updated
---> Package mysql.i686 0:5.5.36-1.el6.remi will be an update
---> Package mysql-libs.i686 0:5.5.35-1.el6.remi will be updated
---> Package mysql-libs.i686 0:5.5.36-1.el6.remi will be an update
---> Package mysql-server.i686 0:5.5.35-1.el6.remi will be updated
---> Package mysql-server.i686 0:5.5.36-1.el6.remi will be an update
---> Package nss.i686 0:3.15.3-3.el6_5 will be updated
---> Package nss.i686 0:3.15.3-6.el6_5 will be an update
---> Package nss-sysinit.i686 0:3.15.3-3.el6_5 will be updated
---> Package nss-sysinit.i686 0:3.15.3-6.el6_5 will be an update
---> Package nss-tools.i686 0:3.15.3-3.el6_5 will be updated

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---> Package nss-tools.i686 0:3.15.3-6.el6_5 will be an update

---> Package openldap.i686 0:2.4.23-32.el6_4.1 will be updated
---> Package openldap.i686 0:2.4.23-34.el6_5.1 will be an update
---> Package p11-kit.i686 0:0.18.5-2.el6 will be updated
---> Package p11-kit.i686 0:0.18.5-2.el6_5.2 will be an update
---> Package p11-kit-trust.i686 0:0.18.5-2.el6 will be updated
---> Package p11-kit-trust.i686 0:0.18.5-2.el6_5.2 will be an update
---> Package perf.i686 0:2.6.32-431.3.1.el6 will be updated
---> Package perf.i686 0:2.6.32-431.5.1.el6 will be an update
---> Package perl-Compress-Raw-Bzip2.i686 0:2.021-136.el6 will be updated
---> Package perl-Compress-Raw-Bzip2.i686 0:2.052-1.el6.rf will be an update
---> Package php.i686 0:5.5.8-1.el6.remi will be updated
---> Package php.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-bcmath.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-bcmath.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-cli.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-cli.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-common.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-common.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-gd.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-gd.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-gmp.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-gmp.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-mbstring.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-mbstring.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-mcrypt.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-mcrypt.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-mysqlnd.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-mysqlnd.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-pdo.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-pdo.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-pecl-zip.i686 0:1.12.3-1.el6.remi.5.5 will be updated
---> Package php-pecl-zip.i686 0:1.12.4-1.el6.remi.5.5 will be an update
---> Package php-process.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-process.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-recode.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-recode.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-tcpdf.noarch 0:6.0.053-1.el6.remi will be updated
---> Package php-tcpdf.noarch 0:6.0.059-1.el6.remi will be an update
---> Package php-tcpdf-dejavu-sans-fonts.noarch 0:6.0.053-1.el6.remi will be updated
---> Package php-tcpdf-dejavu-sans-fonts.noarch 0:6.0.059-1.el6.remi will be an update
---> Package php-tidy.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-tidy.i686 0:5.5.9-2.el6.remi will be an update
---> Package php-xml.i686 0:5.5.8-1.el6.remi will be updated
---> Package php-xml.i686 0:5.5.9-2.el6.remi will be an update

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---> Package phpMyAdmin.noarch 0:4.1.4-1.el6.remi will be updated

---> Package phpMyAdmin.noarch 0:4.1.7-1.el6.remi will be an update
---> Package python.i686 0:2.6.6-51.el6 will be updated
---> Package python.i686 0:2.6.6-52.el6 will be an update
---> Package python-libs.i686 0:2.6.6-51.el6 will be updated
---> Package python-libs.i686 0:2.6.6-52.el6 will be an update
---> Package tzdata.noarch 0:2013i-1.el6 will be updated
---> Package tzdata.noarch 0:2013i-2.el6 will be an update
---> Package tzdata-java.noarch 0:2013i-1.el6 will be updated
---> Package tzdata-java.noarch 0:2013i-2.el6 will be an update
---> Package wget.i686 0:1.12-1.8.el6 will be updated
---> Package wget.i686 0:1.12-1.11.el6_5 will be an update
---> Package yum-plugin-fastestmirror.noarch 0:1.1.30-14.el6 will be updated
---> Package yum-plugin-fastestmirror.noarch 0:1.1.30-17.el6_5 will be an update
---> Package yum-plugin-security.noarch 0:1.1.30-14.el6 will be updated
---> Package yum-plugin-security.noarch 0:1.1.30-17.el6_5 will be an update
---> Package yum-utils.noarch 0:1.1.30-14.el6 will be updated
---> Package yum-utils.noarch 0:1.1.30-17.el6_5 will be an update
--> Finished Dependency Resolution

Dependencies Resolved

================================================================================
Package Arch Version Repository Size
================================================================================
Installing:
kernel i686 2.6.32-431.5.1.el6 updates 26 M
Updating:
bind-libs i686 32:9.8.2-0.23.rc1.el6_5.1 updates 891 k
bind-utils i686 32:9.8.2-0.23.rc1.el6_5.1 updates 181 k
irqbalance i686 2:1.0.4-8.el6_5 updates 38 k
java-1.6.0-openjdk i686 1:1.6.0.0-3.1.13.1.el6_5 updates 42 M
java-1.7.0-openjdk i686 1:1.7.0.51-2.4.4.1.el6_5 updates 27 M
kernel-firmware noarch 2.6.32-431.5.1.el6 updates 13 M
kernel-headers i686 2.6.32-431.5.1.el6 updates 2.8 M
mysql i686 5.5.36-1.el6.remi remi 5.8 M
mysql-libs i686 5.5.36-1.el6.remi remi 778 k
mysql-server i686 5.5.36-1.el6.remi remi 10 M
nss i686 3.15.3-6.el6_5 updates 826 k
nss-sysinit i686 3.15.3-6.el6_5 updates 40 k
nss-tools i686 3.15.3-6.el6_5 updates 368 k
openldap i686 2.4.23-34.el6_5.1 updates 267 k
p11-kit i686 0.18.5-2.el6_5.2 updates 93 k
p11-kit-trust i686 0.18.5-2.el6_5.2 updates 68 k
perf i686 2.6.32-431.5.1.el6 updates 2.9 M

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perl-Compress-Raw-Bzip2 i686 2.052-1.el6.rf rpmforge 101 k

php i686 5.5.9-2.el6.remi remi-php55 2.5 M
php-bcmath i686 5.5.9-2.el6.remi remi-php55 46 k
php-cli i686 5.5.9-2.el6.remi remi-php55 2.5 M
php-common i686 5.5.9-2.el6.remi remi-php55 1.0 M
php-gd i686 5.5.9-2.el6.remi remi-php55 65 k
php-gmp i686 5.5.9-2.el6.remi remi-php55 39 k
php-mbstring i686 5.5.9-2.el6.remi remi-php55 950 k
php-mcrypt i686 5.5.9-2.el6.remi remi-php55 37 k
php-mysqlnd i686 5.5.9-2.el6.remi remi-php55 253 k
php-pdo i686 5.5.9-2.el6.remi remi-php55 104 k
php-pecl-zip i686 1.12.4-1.el6.remi.5.5 remi-php55 273 k
php-process i686 5.5.9-2.el6.remi remi-php55 50 k
php-recode i686 5.5.9-2.el6.remi remi-php55 24 k
php-tcpdf noarch 6.0.059-1.el6.remi remi 1.8 M
php-tcpdf-dejavu-sans-fonts noarch 6.0.059-1.el6.remi remi 84 k
php-tidy i686 5.5.9-2.el6.remi remi-php55 42 k
php-xml i686 5.5.9-2.el6.remi remi-php55 196 k
phpMyAdmin noarch 4.1.7-1.el6.remi remi 4.7 M
python i686 2.6.6-52.el6 updates 74 k
python-libs i686 2.6.6-52.el6 updates 5.3 M
tzdata noarch 2013i-2.el6 updates 448 k
tzdata-java noarch 2013i-2.el6 updates 147 k
wget i686 1.12-1.11.el6_5 updates 482 k
yum-plugin-fastestmirror noarch 1.1.30-17.el6_5 updates 28 k
yum-plugin-security noarch 1.1.30-17.el6_5 updates 38 k
yum-utils noarch 1.1.30-17.el6_5 updates 102 k

Transaction Summary
================================================================================
Install 1 Package(s)
Upgrade 44 Package(s)

Total download size: 154 M

Is this ok [y/N]:

Voila! The error is gone now!

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