TypeError: rpmdb open failed

Red Knuckles · 11-04-2006, 02:06 PM

In recent install [updated once or twice previously] of FC 6 when I try to run 'yum -y update' I get the following output:

# yum -y update
Loading "installonlyn" plugin
rpmdb: PANIC: fatal region error detected; run recovery
error: db4 error(-30977) from dbenv->open: DB_RUNRECOVERY: Fatal error, run database recovery
error: cannot open Packages index using db3 - (-30977)
error: cannot open Packages database in /var/lib/rpm
Traceback (most recent call last):
File "/usr/bin/yum", line 29, in ?
yummain.main(sys.argv[1:])
File "/usr/share/yum-cli/yummain.py", line 85, in main
base.getOptionsConfig(args)
File "/usr/share/yum-cli/cli.py", line 199, in getOptionsConfig
errorlevel=opts.errorlevel)
File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 125, in doConfigSetup
self.conf = config.readMainConfig(startupconf)
File "/usr/lib/python2.4/site-packages/yum/config.py", line 597, in readMainConfig
vars['releasever'] = _getsysver(startupconf.installroot, startupconf.distroverpkg)
File "/usr/lib/python2.4/site-packages/yum/config.py", line 656, in _getsysver
idx = ts.dbMatch('provides', distroverpkg)
TypeError: rpmdb open failed

What's going on and how do I fix??? When I try to edit '/etc/yum.repos.d' as root with kwrite I get:

The file 'file:///etc/yum.repos.d' could not be opened: it is not a normal file, it is a folder.

That seems very wrong to me. How to edit?

When I try '# gedit /etc/yum.repos.d' I get:

Could not open the file /etc/yum.repos.d.

Lenard · 11-04-2006, 02:14 PM

Quote:

The file 'file:///etc/yum.repos.d' could not be opened: it is not a normal file, it is a folder.

This is not an error, it is a warning message. The directory /etc/yum.repo.d is not a file. The same applies for for gedit.

For the yum error, try cleaning the cache; yum clean all

.

Red Knuckles · 11-04-2006, 02:20 PM

Quote:

Originally Posted by Lenard

This is not an error, it is a warning message. The directory /etc/yum.repo.d is not a file. The same applies for for gedit.

For the yum error, try cleaning the cache; yum clean all

.

I did and got this:

# yum clean all
Loading "installonlyn" plugin
rpmdb: PANIC: fatal region error detected; run recovery
error: db4 error(-30977) from dbenv->open: DB_RUNRECOVERY: Fatal error, run database recovery
error: cannot open Packages index using db3 - (-30977)
error: cannot open Packages database in /var/lib/rpm
Traceback (most recent call last):
File "/usr/bin/yum", line 29, in ?
yummain.main(sys.argv[1:])
File "/usr/share/yum-cli/yummain.py", line 85, in main
base.getOptionsConfig(args)
File "/usr/share/yum-cli/cli.py", line 199, in getOptionsConfig
errorlevel=opts.errorlevel)
File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 125, in doConfigSetup
self.conf = config.readMainConfig(startupconf)
File "/usr/lib/python2.4/site-packages/yum/config.py", line 597, in readMainConfig
vars['releasever'] = _getsysver(startupconf.installroot, startupconf.distroverpkg)
File "/usr/lib/python2.4/site-packages/yum/config.py", line 656, in _getsysver
idx = ts.dbMatch('provides', distroverpkg)
TypeError: rpmdb open failed

As far as the warning for '/etc/yum.repo.d' how do I check, edit, or add/remove repos then? Do I have the wrong file? I must because it is a folder?

Red Knuckles · 11-04-2006, 02:52 PM

Ok, I fingered out how to deal with repos in FC 6. Apparently I was used to them all being in one file but now they are in a folder and you have to edit each file seperately. ie. 'kwrite /etc/yum/repos.d/fedora-core.repo' and in my case also '/etc/yum/repos.d/fedora-extras.repo' and '/etc/yum/repos.d/fedora-updates.repo'. For some reason [WHY???] FC 6 comments out all base urls in repos by default [#] so you have to remove the # before the base urls that you wish to have enabled [enabled=1]. In my case so far that is only core, extras and update. I did that but yum still won't run and gives the same error for 'yum clean all'. At least that is what I think I learned from scanning other posts. If I'm wrong someone correct me! I still don't understand why rpmdb open failed??? Is it trying to tell me something when it mentions 'Fatal error, run database recovery' and 'rpmdb: PANIC: fatal region error detected; run recovery'? Aren't I looking for a command to recover the rpmdb? Or am I looking for a rpm command? Will keep looking...

Red Knuckles · 11-04-2006, 03:42 PM

As of my last post I had not rebooted my computer. What solved the problem was removing the '#' from the base urls in repos AND rebooting computer. Then I ran:

# yum clean all
Loading "installonlyn" plugin
Cleaning up Everything
# yum -y update
Loading "installonlyn" plugin
Setting up Update Process
Setting up repositories
core 100% |=========================| 1.1 kB 00:00
updates 100% |=========================| 1.2 kB 00:00
extras 100% |=========================| 1.1 kB 00:00
Reading repository metadata in from local files
primary.xml.gz 100% |=========================| 824 kB 00:02
################################################## 2242/2242
primary.xml.gz 100% |=========================| 81 kB 00:00
################################################## 249/249
primary.xml.gz 100% |=========================| 1.3 MB 00:28
################################################## 4027/4027
Resolving Dependencies
--> Populating transaction set with selected packages. Please wait.
---> Downloading header for kdeadmin to pack into transaction set.
kdeadmin-3.5.5-0.1.fc6.i3 100% |=========================| 35 kB 00:00

so it appears as if it's going to update. Looks like a long one too. Maybe I never updated my FC 6 install yet afterall...

Red Knuckles · 11-04-2006, 04:57 PM

Quote:

Originally Posted by Red Knuckles

As of my last post I had not rebooted my computer. What solved the problem was removing the '#' from the base urls in repos AND rebooting computer. Then I ran:

# yum clean all
Loading "installonlyn" plugin
Cleaning up Everything
# yum -y update
Loading "installonlyn" plugin
Setting up Update Process
Setting up repositories
core 100% |=========================| 1.1 kB 00:00
updates 100% |=========================| 1.2 kB 00:00
extras 100% |=========================| 1.1 kB 00:00
Reading repository metadata in from local files
primary.xml.gz 100% |=========================| 824 kB 00:02
################################################## 2242/2242
primary.xml.gz 100% |=========================| 81 kB 00:00
################################################## 249/249
primary.xml.gz 100% |=========================| 1.3 MB 00:28
################################################## 4027/4027
Resolving Dependencies
--> Populating transaction set with selected packages. Please wait.
---> Downloading header for kdeadmin to pack into transaction set.
kdeadmin-3.5.5-0.1.fc6.i3 100% |=========================| 35 kB 00:00

so it appears as if it's going to update. Looks like a long one too. Maybe I never updated my FC 6 install yet afterall...

I spoke to soon. When I do the above yum updates a few packages and then I get I very long list like this:

rpmdb: PANIC: fatal region error detected; run recovery
error: db4 error(-30977) from db->sync: DB_RUNRECOVERY: Fatal error, run database recovery
rpmdb: PANIC: fatal region error detected; run recovery
error: db4 error(-30977) from db->sync: DB_RUNRECOVERY: Fatal error, run database recovery
rpmdb: PANIC: fatal region error detected; run recovery
error: db4 error(-30977) from db->sync: DB_RUNRECOVERY: Fatal error, run database recovery
rpmdb: PANIC: fatal region error detected; run recovery
error: db4 error(-30977) from db->sync: DB_RUNRECOVERY: Fatal error, run database recovery
rpmdb: PANIC: fatal region error detected; run recovery
error: db4 error(-30977) from db->sync: DB_RUNRECOVERY: Fatal error, run database recovery
rpmdb: PANIC: fatal region error detected; run recovery
error: db4 error(-30977) from db->sync: DB_RUNRECOVERY: Fatal error, run database recovery
rpmdb: PANIC: fatal region error detected; run recovery
error: db4 error(-30977) from db->sync: DB_RUNRECOVERY: Fatal error, run database recovery
rpmdb: PANIC: fatal region error detected; run recovery
error: db4 error(-30977) from db->sync: DB_RUNRECOVERY: Fatal error, run database recovery
rpmdb: PANIC: fatal region error detected; run recovery

and I'm back to 'rpmdb open failed'. Then I reboot and do it again and it updates a few more packages and the same error again. How to fix? I thought that when yum was updating it was accessing repos over the internet. I'm confused as to where the error is. For what it's worth:

# ls /var/lib/rpm
Basenames __db.000 __db.002 Dirnames Group Name Providename Pubkeys Requireversion Sigmd5
Conflictname __db.001 __db.003 Filemd5s Installtid Packages Provideversion Requirename Sha1header Triggername

Red Knuckles · 11-04-2006, 05:15 PM

Is it possible that the repos themselves are the problem? These are the 3 I have enabled:

[core]
name=Fedora Core $releasever - $basearch
baseurl=http://download.fedora.redhat.com/pub/fedora/linux/core/$releasever/$basearch/os/
mirrorlist=http://mirrors.fedoraproject.org/mirrorlist?repo=core-$releasever&arch=$basearch
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora file:///etc/pki/rpm-gpg/RPM-GPG-KEY

[extras]
name=Fedora Extras $releasever - $basearch
baseurl=http://download.fedora.redhat.com/pub/fedora/linux/extras/$releasever/$basearch/
mirrorlist=http://mirrors.fedoraproject.org/mirrorlist?repo=extras-$releasever&arch=$basearch
enabled=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora-extras
gpgcheck=1

[updates]
name=Fedora Core $releasever - $basearch - Updates
baseurl=http://download.fedora.redhat.com/pub/fedora/linux/core/updates/$releasever/$basearch/
mirrorlist=http://mirrors.fedoraproject.org/mirrorlist?repo=updates-released-fc$releasever&arch=$basearch
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora

Lenard · 11-04-2006, 07:37 PM

Yes, not only is this possible but very likely....... they are still working on getting everything back right after a near fatal overload/crash when FC6 was released.

Place a pound sign (#) at the start of all three baseurl lines, example;

#baseurl=http://download.fedora.redhat.com/pub/fedora/linux/core/$releasever/$basearch/os/

This line is wrong (the core section);
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora file:///etc/pki/rpm-gpg/RPM-GPG-KEY

it should read like the other two.

.

Red Knuckles · 11-05-2006, 01:40 PM

Quote:

Originally Posted by Lenard

Yes, not only is this possible but very likely....... they are still working on getting everything back right after a near fatal overload/crash when FC6 was released.

Place a pound sign (#) at the start of all three baseurl lines, example;

#baseurl=http://download.fedora.redhat.com/pub/fedora/linux/core/$releasever/$basearch/os/

This line is wrong (the core section);
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora file:///etc/pki/rpm-gpg/RPM-GPG-KEY

it should read like the other two.

.

I got the solution to this problem from 2 different forums. I replaced the # sign in front of the 3 base urls where I had removed them. Also corrected the 'gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora file:///etc/pki/rpm-gpg/RPM-GPG-KEY'
line to read
'gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora'
in the 'core' repos.

Then I ran:

# rm /var/lib/rpm/__db*
# rpm --rebuilddb
# yum -y update

and it updated 29 packages without error or warning. Thanks Lenard [LinuxQuestions.org]. Thanks timdsmith [Fedora Forum].