Cannot query rpm packages or perform updates with yum anymore

SycronTW · 11-19-2015, 04:30 PM

Hi,

I cannot query the installed or update packages on my CentOS system anymore.
I get the following

Code:

rpm -qa
gpg-pubkey-a0bdbcf9-42d1d837
gpg-pubkey-ef1d6db8-4e0fd7f0
gpg-pubkey-6b8d79e6-3f49313d
gpg-pubkey-c105b9de-4e0fd3a3
gpg-pubkey-d0ff3d16-4e0fd442
gpg-pubkey-0608b895-4bd22942
gpg-pubkey-11f63c51-3c7dc11d
gpg-pubkey-fe837f6f-4e0fd77e

Code:

uname -a
Linux myserver.local 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

Code:

cat /etc/redhat-release
CentOS release 6.6 (Final)

Code:

yum update
Loaded plugins: fastestmirror, security
Loading mirror speeds from cached hostfile
 * base: mirror.myip.be
 * epel: ftp.nluug.nl
 * extras: mirror.myip.be
 * updates: mirror.myip.be
Setting up Update Process
No Packages marked for Update

Code:

cat /etc/yum.conf
[main]
cachedir=/var/cache/yum/$basearch/$releasever
keepcache=0
debuglevel=2
logfile=/var/log/yum.log
exactarch=1
obsoletes=1
gpgcheck=0
plugins=1
installonly_limit=5
bugtracker_url=http://bugs.centos.org/set_project.php?project_id=16&ref=http://bugs.centos.org/bug_report_page.php?category=yum
distroverpkg=centos-release

#  This is the default, if you make this bigger yum won't see if the metadata
# is newer on the remote and so you'll "gain" the bandwidth of not having to
# download the new metadata and "pay" for it by yum not having correct
# information.
#  It is esp. important, to have correct metadata, for distributions like
# Fedora which don't keep old packages around. If you don't like this checking
# interupting your command line usage, it's much better to have something
# manually check the metadata once an hour (yum-updatesd will do this).
# metadata_expire=90m

# PUT YOUR REPOS HERE OR IN separate files named file.repo
# in /etc/yum.repos.d

Code:

 ll /etc/yum.repos.d/
total 56
-rw-r--r--  1 root root 2288 Feb  1  2015 CentOS-Base.repo
-rw-r--r--  1 root root  647 Oct 23  2014 CentOS-Debuginfo.repo
-rw-r--r--  1 root root  289 Oct 23  2014 CentOS-fasttrack.repo
-rw-r--r--  1 root root  630 Oct 23  2014 CentOS-Media.repo
-rw-r--r--  1 root root 5394 Oct 23  2014 CentOS-Vault.repo
-rw-r--r--  1 root root  956 Jan 29  2015 epel.repo
-rw-r--r--  1 root root 1056 Nov  5  2012 epel-testing.repo
-rw-r--r--  1 root root  739 Mar 20  2013 mirrors-rpmforge
-rw-r--r--  1 root root  717 Mar 20  2013 mirrors-rpmforge-extras
-rw-r--r--  1 root root  728 Mar 20  2013 mirrors-rpmforge-testing
-rw-r--r--  1 root root 1128 Jan 29  2015 rpmforge.repo
-rwxr-x---  1 root root  556 Nov 19 22:56 virtualmin.repo
-rw-r--r--. 1 root root  100 Feb  1  2015 webmin.repo

Can anyone help me out pls ?

chrism01 · 11-19-2015, 06:08 PM

Can you run

Code:

yum repolist

to see which ones are actually active/enabled?

Have you installed & setup https://wiki.centos.org/PackageManag...Yum/Priorities ? If not that could be the problem.

berndbausch · 11-19-2015, 06:17 PM

To be honest, I don't see any error. "No Packages marked for Update" is not an error message; your system might be up to date.

Or is this the entire output of rpm -qa? If yes, your rpm database under /var/lib/rpm has a problem.

gpg-pubkey-a0bdbcf9-42d1d837
gpg-pubkey-ef1d6db8-4e0fd7f0
gpg-pubkey-6b8d79e6-3f49313d
gpg-pubkey-c105b9de-4e0fd3a3
gpg-pubkey-d0ff3d16-4e0fd442
gpg-pubkey-0608b895-4bd22942
gpg-pubkey-11f63c51-3c7dc11d
gpg-pubkey-fe837f6f-4e0fd77e

John VV · 11-19-2015, 06:31 PM

centos 6.6 is NOT supported any longer
only the current minor version is supported

for the older 6 series that is CentOS 6.7

as above please post the output of " yum repolist all "

posting the file names of what is in "/etc/yum.repos.d/" is of no real value
we DO NOT know if any or ALL are turned ON or OFF !!
the " repolist all "command WILL tell us that

also BE AWARE that "the vault" is for UNSUPPORTED old UNPATCHED software
the code in the historical archive will NEVER be updated

Quote:

cat /etc/redhat-release
CentOS release 6.6 (Final)

that however IS A PROBLEM

6.6 is not supported

if cent is set up to use the /6 repos then it should auto upgrade -- not the default setting
if you set up cent to use the /6.6 repos there are NO updates

please upgrade to a supported version ASAP

if your repo files are using the default mirror string
"/$releasever/$basearch/os/"
then

Code:

su -
yum --releasever=6.7 upgrade

berndbausch · 11-19-2015, 06:38 PM

Quote:

Originally Posted by John VV

please upgrade to a supported version ASAP

I guess this is what the OP is trying to do:

Code:

yum update
Loaded plugins: fastestmirror, security
Loading mirror speeds from cached hostfile
 * base: mirror.myip.be
 * epel: ftp.nluug.nl
 * extras: mirror.myip.be
 * updates: mirror.myip.be
Setting up Update Process
No Packages marked for Update

SycronTW · 11-20-2015, 01:57 AM

Hi thank you all for the quick responses !
Here's some extra information :

Code:

yum repolist
Loaded plugins: fastestmirror, security
Loading mirror speeds from cached hostfile
 * base: mirror.myip.be
 * epel: ftp.nluug.nl
 * extras: mirror.myip.be
 * updates: mirror.myip.be
repo id                                                                            repo name                                                                                                              status
Webmin                                                                             Webmin Distribution Neutral                                                                                               229
base                                                                               CentOS-$releasever - Base                                                                                               6,575
epel                                                                               Extra Packages for Enterprise Linux 6 - x86_64                                                                         11,866
extras                                                                             CentOS-$releasever - Extras                                                                                                45
updates                                                                            CentOS-$releasever - Updates                                                                                              670
virtualmin                                                                         RHEL/CentOS/Scientific $releasever - x86_64 - Virtualmin                                                                  130
virtualmin-universal                                                               Virtualmin Distribution Neutral Packages                                                                                   55
repolist: 19,570

Code:

# yum --releasever=6.7 upgrade
Loaded plugins: fastestmirror, security
Determining fastest mirrors
epel/metalink                                                                                                                                                                            |  25 kB     00:00
 * base: mirror.myip.be
 * epel: mirrors.coreix.net
 * extras: mirror.myip.be
 * updates: mirror.myip.be
Webmin                                                                                                                                                                                   | 1.0 kB     00:00
Webmin/primary                                                                                                                                                                           |  29 kB     00:00
Webmin                                                                                                                                                                                                  229/229
base                                                                                                                                                                                     | 3.7 kB     00:00
base/primary_db                                                                                                                                                                          | 4.6 MB     00:00
epel                                                                                                                                                                                     | 4.3 kB     00:00
epel/primary_db                                                                                                                                                                          | 5.7 MB     00:00
extras                                                                                                                                                                                   | 3.4 kB     00:00
extras/primary_db                                                                                                                                                                        |  33 kB     00:00
updates                                                                                                                                                                                  | 3.4 kB     00:00
updates/primary_db                                                                                                                                                                       | 2.6 MB     00:00
virtualmin                                                                                                                                                                               | 1.2 kB     00:00
virtualmin/primary                                                                                                                                                                       |  38 kB     00:00
virtualmin                                                                                                                                                                                              130/130
virtualmin-universal                                                                                                                                                                     | 1.2 kB     00:00
virtualmin-universal/primary                                                                                                                                                             | 8.2 kB     00:00
virtualmin-universal                                                                                                                                                                                      55/55
Setting up Upgrade Process
No Packages marked for Update

Last updates were installed on 28/01/15

Code:

# tail /var/log/yum.log
Jan 28 14:54:28 Updated: 1:net-snmp-utils-5.5-50.el6_6.1.x86_64
Jan 28 14:54:28 Updated: 1:net-snmp-5.5-50.el6_6.1.x86_64
Jan 28 14:54:32 Updated: 1:nfs-utils-1.2.3-54.el6.x86_64
Jan 28 14:54:37 Updated: nfs-utils-lib-1.1.5-9.el6.x86_64
Jan 28 14:54:41 Updated: 2:nmap-5.51-4.el6.x86_64
Jan 28 14:54:45 Updated: nss-util-3.16.2.3-2.el6_6.x86_64
Jan 28 14:54:45 Updated: nss-sysinit-3.16.2.3-3.el6_6.x86_64
Jan 28 14:54:45 Updated: nss-3.16.2.3-3.el6_6.x86_64
Jan 28 14:54:45 Updated: nss-tools-3.16.2.3-3.el6_6.x86_64
Jan 28 14:54:48 Updated: nss-softokn-3.14.3-19.el6_6.x86_64

What else can I check pls ?
I have already deleted the rpm DB in /var/lib/rpm and recreated it with rpm --rebuilddb -vv without any success
The only output I get on rpm -qa is

Code:

# rpm -qa
gpg-pubkey-a0bdbcf9-42d1d837
gpg-pubkey-ef1d6db8-4e0fd7f0
gpg-pubkey-6b8d79e6-3f49313d
gpg-pubkey-c105b9de-4e0fd3a3
gpg-pubkey-d0ff3d16-4e0fd442
gpg-pubkey-0608b895-4bd22942
gpg-pubkey-11f63c51-3c7dc11d
gpg-pubkey-fe837f6f-4e0fd77e

berndbausch · 11-20-2015, 02:43 AM

From the rpm man page:

Quote:

use --rebuilddb to rebuild the database indices from the installed package headers

If you have no package headers, rebuilddb won't be too useful.

Do you have a backup?

SycronTW · 11-20-2015, 09:47 AM

Hi Bernd,

I don't have a backup of the system.
I have tried the --rebuilddb withour any succes

Code:

#rpm --rebuilddb
[root@myserver~]# rpm -qa
gpg-pubkey-ef1d6db8-4e0fd7f0
gpg-pubkey-c105b9de-4e0fd3a3
gpg-pubkey-0608b895-4bd22942
gpg-pubkey-fe837f6f-4e0fd77e
gpg-pubkey-a0bdbcf9-42d1d837
gpg-pubkey-6b8d79e6-3f49313d
gpg-pubkey-d0ff3d16-4e0fd442
gpg-pubkey-11f63c51-3c7dc11d

# ll /var/lib/rpm/
total 14588
-rw-r--r--. 1 root root  5820416 Jan 28  2015 Basenames
-rw-r--r--. 1 root root    12288 Jan 28  2015 Conflictname
-rw-r--r--  1 root root    24576 Nov 20 16:46 __db.001
-rw-r--r--  1 root root   229376 Nov 20 16:46 __db.002
-rw-r--r--  1 root root  1318912 Nov 20 16:46 __db.003
-rw-r--r--  1 root root   753664 Nov 20 16:46 __db.004
-rw-r--r--. 1 root root  1400832 Jan 28  2015 Dirnames
-rw-r--r--. 1 root root 10211328 Jan 28  2015 Filedigests
-rw-r--r--  1 root root    12288 Jan 28  2015 Group
-rw-r--r--  1 root root     8192 Jan 28  2015 Installtid
-rw-r--r--  1 root root    12288 Jan 28  2015 Name
-rw-r--r--. 1 root root    12288 Jan 28  2015 Obsoletename
drwxr-xr-x  2 root root     4096 Jan 29  2015 old
-rw-r--r--  1 root root    45056 Jan 28  2015 Packages
-rw-r--r--  1 root root    12288 Jan 28  2015 Providename
-rw-r--r--  1 root root     8192 Jan 28  2015 Provideversion
-rw-r--r--  1 root root    12288 Jan 29  2015 Pubkeys
-rw-r--r--. 1 root root   425984 Jan 28  2015 Requirename
-rw-r--r--. 1 root root   200704 Jan 28  2015 Requireversion
-rw-r--r--. 1 root root    94208 Jan 28  2015 Sha1header
-rw-r--r--. 1 root root    49152 Jan 28  2015 Sigmd5
-rw-r--r--. 1 root root    12288 Jan 28  2015 Triggername

SycronTW · 11-23-2015, 06:32 AM

Problem was caued by a failing update of nss-softokn-3-14-3-19-el6_6
I solved the problem with yum & rppm by following the instructions in the post below
http://kiteplans.info/2015/01/15/sol...omment-page-2/

ilesterg · 11-23-2015, 09:32 PM

Hi,

Glad you figured out how to fix the problem. Sorry but I wanted a takeaway on your thread, I understand that you have a broken rpmdb based on your rpm -qa output, so I want to ask how you figured out the problem is with a failed nss-softokn update? The link mentions the error "error: rpmts_HdrFromFdno: Header V3 RSA/SHA1 Signature, key ID xxx BAD

error: rpmdbNextIterator: skipping h# 1784 Header V3 RSA/SHA1 Signature, key ID xxx BAD", which is supposed to appear when you try to yum update, but it did not.

Cheers.

SycronTW · 11-24-2015, 04:18 AM

I figured it out because nss-softokn-3.14.3-19.el6_6.x86_64 was the last rpm package that was updated according to /var/log/yum.log.

Code:

# tail /var/log/yum.log
Jan 28 14:54:28 Updated: 1:net-snmp-utils-5.5-50.el6_6.1.x86_64
Jan 28 14:54:28 Updated: 1:net-snmp-5.5-50.el6_6.1.x86_64
Jan 28 14:54:32 Updated: 1:nfs-utils-1.2.3-54.el6.x86_64
Jan 28 14:54:37 Updated: nfs-utils-lib-1.1.5-9.el6.x86_64
Jan 28 14:54:41 Updated: 2:nmap-5.51-4.el6.x86_64
Jan 28 14:54:45 Updated: nss-util-3.16.2.3-2.el6_6.x86_64
Jan 28 14:54:45 Updated: nss-sysinit-3.16.2.3-3.el6_6.x86_64
Jan 28 14:54:45 Updated: nss-3.16.2.3-3.el6_6.x86_64
Jan 28 14:54:45 Updated: nss-tools-3.16.2.3-3.el6_6.x86_64
Jan 28 14:54:48 Updated: nss-softokn-3.14.3-19.el6_6.x86_64

At that time I had received an error during the update but since I never had any issues during yum updates I didn't really look into it at that time
Google did the rest ;-)