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:
# 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 ---> 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 ---> 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  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!
