rpmdb: PANIC: fatal region error detected; run recovery
error: db3 error(-30974) from dbenv->open: DB_RUNRECOVERY: Fatal error, run database recovery
error: cannot open Packages index using db3 - (-30974)
error: cannot open Packages database in /var/lib/rpm
CRITICAL:yum.main:Error: rpmdb open failed
How do I fix this problem on a CentOS / RHEL based system?
mkdir /root/backups.rpm.mm_dd_yyyy/
cp -avr /var/lib/rpm/ /root/backups.rpm.mm_dd_yyyy/
To find list of __db* file, enter:
Sample outputs:
cp -avr /var/lib/rpm/ /root/backups.rpm.mm_dd_yyyy/
To find list of __db* file, enter:
# ls -l /var/lib/rpm/_*Sample outputs:
-rw-r--r-- 1 root root 24576 Jan 28 04:00 /var/lib/rpm/__db.001 -rw-r--r-- 1 root root 229376 Jan 28 04:00 /var/lib/rpm/__db.002 -rw-r--r-- 1 root root 1318912 Jan 28 04:00 /var/lib/rpm/__db.003 -rw-r--r-- 1 root root 753664 Jan 28 04:00 /var/lib/rpm/__db.004
To fix this problem, try:
Verify that error has gone with the following yum command
Sample outputs:
# rm -f /var/lib/rpm/__db*
# db_verify /var/lib/rpm/Packages
# rpm --rebuilddb
# yum clean allVerify that error has gone with the following yum command
# yum updateSample outputs:
Loaded plugins: downloadonly, fastestmirror, security Determining fastest mirrors * base: centos.mirrors.tds.net * extras: centos.corenetworks.net * updates: mirror.fdcservers.net base | 3.7 kB 00:00 base/primary_db | 4.4 MB 00:00 extras | 3.4 kB 00:00 extras/primary_db | 19 kB 00:00 updates | 3.4 kB 00:00 updates/primary_db | 2.0 MB 00:00 Setting up Update Process Resolving Dependencies --> Running transaction check ---> Package kernel.x86_64 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 mysql-libs.x86_64 0:5.1.71-1.el6 will be updated ---> Package mysql-libs.x86_64 0:5.1.73-3.el6_5 will be an update ---> Package nss.x86_64 0:3.15.3-3.el6_5 will be updated ---> Package nss.x86_64 0:3.15.3-6.el6_5 will be an update ---> Package nss-sysinit.x86_64 0:3.15.3-3.el6_5 will be updated ---> Package nss-sysinit.x86_64 0:3.15.3-6.el6_5 will be an update ---> Package nss-tools.x86_64 0:3.15.3-3.el6_5 will be updated ---> Package nss-tools.x86_64 0:3.15.3-6.el6_5 will be an update ---> Package openldap.x86_64 0:2.4.23-32.el6_4.1 will be updated ---> Package openldap.x86_64 0:2.4.23-34.el6_5.1 will be an update ---> Package p11-kit.x86_64 0:0.18.5-2.el6 will be updated ---> Package p11-kit.x86_64 0:0.18.5-2.el6_5.2 will be an update ---> Package p11-kit-trust.x86_64 0:0.18.5-2.el6 will be updated ---> Package p11-kit-trust.x86_64 0:0.18.5-2.el6_5.2 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 wget.x86_64 0:1.12-1.8.el6 will be updated ---> Package wget.x86_64 0:1.12-1.11.el6_5 will be an update ---> Package yum-plugin-downloadonly.noarch 0:1.1.30-14.el6 will be updated ---> Package yum-plugin-downloadonly.noarch 0:1.1.30-17.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 --> Running transaction check ---> Package kernel.x86_64 0:2.6.32-358.18.1.el6 will be erased --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: kernel x86_64 2.6.32-431.5.1.el6 updates 28 M Updating: kernel-firmware noarch 2.6.32-431.5.1.el6 updates 13 M mysql-libs x86_64 5.1.73-3.el6_5 updates 1.2 M nss x86_64 3.15.3-6.el6_5 updates 822 k nss-sysinit x86_64 3.15.3-6.el6_5 updates 40 k nss-tools x86_64 3.15.3-6.el6_5 updates 358 k openldap x86_64 2.4.23-34.el6_5.1 updates 265 k p11-kit x86_64 0.18.5-2.el6_5.2 updates 94 k p11-kit-trust x86_64 0.18.5-2.el6_5.2 updates 71 k tzdata noarch 2013i-2.el6 updates 448 k wget x86_64 1.12-1.11.el6_5 updates 483 k yum-plugin-downloadonly noarch 1.1.30-17.el6_5 updates 21 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 Removing: kernel x86_64 2.6.32-358.18.1.el6 @updates 116 M Transaction Summary ================================================================================ Install 1 Package(s) Upgrade 14 Package(s) Remove 1 Package(s) Total download size: 45 M Is this ok [y/N]: y Downloading Packages: (1/15): kernel-2.6.32-431.5.1.el6.x86_64.rpm | 28 MB 00:01 (2/15): kernel-firmware-2.6.32-431.5.1.el6.noarch.rpm | 13 MB 00:00 (3/15): mysql-libs-5.1.73-3.el6_5.x86_64.rpm | 1.2 MB 00:00 (4/15): nss-3.15.3-6.el6_5.x86_64.rpm | 822 kB 00:00 (5/15): nss-sysinit-3.15.3-6.el6_5.x86_64.rpm | 40 kB 00:00 (6/15): nss-tools-3.15.3-6.el6_5.x86_64.rpm | 358 kB 00:00 (7/15): openldap-2.4.23-34.el6_5.1.x86_64.rpm | 265 kB 00:00 (8/15): p11-kit-0.18.5-2.el6_5.2.x86_64.rpm | 94 kB 00:00 (9/15): p11-kit-trust-0.18.5-2.el6_5.2.x86_64.rpm | 71 kB 00:00 (10/15): tzdata-2013i-2.el6.noarch.rpm | 448 kB 00:00 (11/15): wget-1.12-1.11.el6_5.x86_64.rpm | 483 kB 00:00 (12/15): yum-plugin-downloadonly-1.1.30-17.el6_5.noarch. | 21 kB 00:00 (13/15): yum-plugin-fastestmirror-1.1.30-17.el6_5.noarch | 28 kB 00:00 (14/15): yum-plugin-security-1.1.30-17.el6_5.noarch.rpm | 38 kB 00:00 (15/15): yum-utils-1.1.30-17.el6_5.noarch.rpm | 102 kB 00:00 -------------------------------------------------------------------------------- Total 18 MB/s | 45 MB 00:02 Running rpm_check_debug Running Transaction Test Transaction Test Succeeded Running Transaction Warning: RPMDB altered outside of yum. ** Found 1 pre-existing rpmdb problem(s), 'yum check' output follows: 2:irqbalance-1.0.4-8.el6_5.x86_64 is a duplicate with 2:irqbalance-1.0.4-6.el6.x86_64 Updating : nss-sysinit-3.15.3-6.el6_5.x86_64 1/30 Updating : nss-3.15.3-6.el6_5.x86_64 2/30 Updating : nss-tools-3.15.3-6.el6_5.x86_64 3/30 Updating : p11-kit-0.18.5-2.el6_5.2.x86_64 4/30 Updating : kernel-firmware-2.6.32-431.5.1.el6.noarch 5/30 Installing : kernel-2.6.32-431.5.1.el6.x86_64 6/30 Updating : p11-kit-trust-0.18.5-2.el6_5.2.x86_64 7/30 Updating : openldap-2.4.23-34.el6_5.1.x86_64 8/30 Updating : wget-1.12-1.11.el6_5.x86_64 9/30 Updating : yum-plugin-fastestmirror-1.1.30-17.el6_5.noarch 10/30 Updating : mysql-libs-5.1.73-3.el6_5.x86_64 11/30 Updating : yum-plugin-downloadonly-1.1.30-17.el6_5.noarch 12/30 Updating : yum-utils-1.1.30-17.el6_5.noarch 13/30 Updating : yum-plugin-security-1.1.30-17.el6_5.noarch 14/30 Updating : tzdata-2013i-2.el6.noarch 15/30 Cleanup : kernel-2.6.32-358.18.1.el6.x86_64 16/30 Cleanup : kernel-firmware-2.6.32-431.3.1.el6.noarch 17/30 Cleanup : yum-plugin-fastestmirror-1.1.30-14.el6.noarch 18/30 Cleanup : yum-plugin-downloadonly-1.1.30-14.el6.noarch 19/30 Cleanup : yum-utils-1.1.30-14.el6.noarch 20/30 Cleanup : yum-plugin-security-1.1.30-14.el6.noarch 21/30 Cleanup : tzdata-2013i-1.el6.noarch 22/30 Cleanup : openldap-2.4.23-32.el6_4.1.x86_64 23/30 Cleanup : nss-tools-3.15.3-3.el6_5.x86_64 24/30 Cleanup : nss-sysinit-3.15.3-3.el6_5.x86_64 25/30 Cleanup : nss-3.15.3-3.el6_5.x86_64 26/30 Cleanup : p11-kit-trust-0.18.5-2.el6.x86_64 27/30 Cleanup : p11-kit-0.18.5-2.el6.x86_64 28/30 Cleanup : wget-1.12-1.8.el6.x86_64 29/30 Cleanup : mysql-libs-5.1.71-1.el6.x86_64 30/30 Removed: kernel.x86_64 0:2.6.32-358.18.1.el6 Installed: kernel.x86_64 0:2.6.32-431.5.1.el6 Updated: kernel-firmware.noarch 0:2.6.32-431.5.1.el6 mysql-libs.x86_64 0:5.1.73-3.el6_5 nss.x86_64 0:3.15.3-6.el6_5 nss-sysinit.x86_64 0:3.15.3-6.el6_5 nss-tools.x86_64 0:3.15.3-6.el6_5 openldap.x86_64 0:2.4.23-34.el6_5.1 p11-kit.x86_64 0:0.18.5-2.el6_5.2 p11-kit-trust.x86_64 0:0.18.5-2.el6_5.2 tzdata.noarch 0:2013i-2.el6 wget.x86_64 0:1.12-1.11.el6_5 yum-plugin-downloadonly.noarch 0:1.1.30-17.el6_5 yum-plugin-fastestmirror.noarch 0:1.1.30-17.el6_5 yum-plugin-security.noarch 0:1.1.30-17.el6_5 yum-utils.noarch 0:1.1.30-17.el6_5 Complete!
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