Issues with yum after out of memory error

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littleguy
Posts: 2
Joined: 2013/12/03 21:33:35

Issues with yum after out of memory error

Post by littleguy » 2013/12/03 21:37:31

I had an out of memory error when running yum update to go from CentOS 6.4 to 6.5, and now my yum is broken beyond repairs it seems...

Here is what I get from running you update:

Code: Select all

[root@cdn rpm]# yum update
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: ftp.sunet.se
 * epel: ftp.lysator.liu.se
 * extras: ftp.sunet.se
 * updates: ftp.sunet.se
Setting up Update Process
Resolving Dependencies
--> Running transaction check
---> Package coreutils.x86_64 0:8.4-19.el6_4.2 will be updated
--> Processing Dependency: coreutils = 8.4-19.el6_4.2 for package: coreutils-libs-8.4-19.el6_4.2.x86_64
---> Package coreutils.x86_64 0:8.4-31.el6 will be an update
---> Package cronie.x86_64 0:1.4.4-7.el6 will be updated
---> Package cronie.x86_64 0:1.4.4-12.el6 will be an update
---> Package cronie-noanacron.x86_64 0:1.4.4-7.el6 will be updated
---> Package cronie-noanacron.x86_64 0:1.4.4-12.el6 will be an update
---> Package gcc-c++.x86_64 0:4.4.7-3.el6 will be updated
---> Package gcc-c++.x86_64 0:4.4.7-4.el6 will be an update
---> Package glib2.i686 0:2.22.5-7.el6 will be updated
---> Package glib2.i686 0:2.26.1-3.el6 will be an update
---> Package glibc.i686 0:2.12-1.107.el6_4.5 will be updated
---> Package glibc.i686 0:2.12-1.132.el6 will be an update
---> Package glibc-headers.x86_64 0:2.12-1.107.el6_4.5 will be updated
--> Processing Dependency: glibc-headers = 2.12-1.107.el6_4.5 for package: glibc-devel-2.12-1.107.el6_4.5.x86_64
---> Package glibc-headers.x86_64 0:2.12-1.132.el6 will be an update
---> Package initscripts.x86_64 0:9.03.38-1.el6.centos.2 will be updated
---> Package initscripts.x86_64 0:9.03.40-2.el6.centos will be an update
---> Package iproute.x86_64 0:2.6.32-23.el6 will be updated
---> Package iproute.x86_64 0:2.6.32-31.el6 will be an update
---> Package iptables.x86_64 0:1.4.7-9.el6 will be updated
---> Package iptables.x86_64 0:1.4.7-11.el6 will be an update
---> Package kernel-devel.x86_64 0:2.6.32-431.el6 will be installed
---> Package libcom_err.i686 0:1.41.12-14.el6_4.4 will be updated
---> Package libcom_err.i686 0:1.41.12-18.el6 will be an update
---> Package libgcc.i686 0:4.4.7-3.el6 will be updated
---> Package libgcc.i686 0:4.4.7-4.el6 will be an update
---> Package libpcap.x86_64 14:1.0.0-6.20091201git117cb5.el6 will be updated
---> Package libpcap.x86_64 14:1.4.0-1.20130826git2dbcaa1.el6 will be an update
---> Package libstdc++.i686 0:4.4.7-3.el6 will be updated
---> Package libstdc++.i686 0:4.4.7-4.el6 will be an update
---> Package libxml2.i686 0:2.7.6-12.el6_4.1 will be updated
---> Package libxml2.i686 0:2.7.6-14.el6 will be an update
---> Package mailx.x86_64 0:12.4-6.el6 will be updated
---> Package mailx.x86_64 0:12.4-7.el6 will be an update
---> Package nscd.x86_64 0:2.12-1.107.el6_4.5 will be updated
---> Package nscd.x86_64 0:2.12-1.132.el6 will be an update
---> Package nss-softokn-freebl.i686 0:3.14.3-3.el6_4 will be updated
---> Package nss-softokn-freebl.i686 0:3.14.3-9.el6 will be an update
---> Package nss-tools.x86_64 0:3.14.3-4.el6_4 will be updated
---> Package nss-tools.x86_64 0:3.15.1-15.el6 will be an update
---> Package openssh.x86_64 0:5.3p1-84.1.el6 will be updated
---> Package openssh.x86_64 0:5.3p1-94.el6 will be an update
---> Package openssh-clients.x86_64 0:5.3p1-84.1.el6 will be updated
---> Package openssh-clients.x86_64 0:5.3p1-94.el6 will be an update
---> Package openssh-server.x86_64 0:5.3p1-84.1.el6 will be updated
---> Package openssh-server.x86_64 0:5.3p1-94.el6 will be an update
---> Package perl-Time-HiRes.x86_64 4:1.9721-131.el6_4 will be updated
---> Package perl-Time-HiRes.x86_64 4:1.9721-136.el6 will be an update
---> Package php-cli.x86_64 0:5.3.3-23.el6_4 will be updated
---> Package php-cli.x86_64 0:5.3.3-26.el6 will be an update
---> Package php-fpm.x86_64 0:5.3.3-23.el6_4 will be updated
---> Package php-fpm.x86_64 0:5.3.3-26.el6 will be an update
---> Package python-urlgrabber.noarch 0:3.9.1-8.el6 will be updated
---> Package python-urlgrabber.noarch 0:3.9.1-9.el6 will be an update
---> Package quota.x86_64 1:3.17-18.el6 will be updated
---> Package quota.x86_64 1:3.17-20.el6 will be an update
---> Package rpm-python.x86_64 0:4.8.0-32.el6 will be updated
---> Package rpm-python.x86_64 0:4.8.0-37.el6 will be an update
---> Package rsyslog.x86_64 0:5.8.10-7.el6_4 will be updated
---> Package rsyslog.x86_64 0:5.8.10-8.el6 will be an update
---> Package sudo.x86_64 0:1.8.6p3-7.el6 will be updated
---> Package sudo.x86_64 0:1.8.6p3-12.el6 will be an update
---> Package udev.x86_64 0:147-2.46.el6_4.2 will be updated
---> Package udev.x86_64 0:147-2.51.el6 will be an update
---> Package util-linux-ng.x86_64 0:2.17.2-12.9.el6_4.3 will be updated
---> Package util-linux-ng.x86_64 0:2.17.2-12.14.el6 will be an update
--> Finished Dependency Resolution
--> Running transaction check
---> Package coreutils.x86_64 0:8.4-19.el6_4.2 will be updated
--> Processing Dependency: coreutils = 8.4-19.el6_4.2 for package: coreutils-libs-8.4-19.el6_4.2.x86_64
---> Package glibc-headers.x86_64 0:2.12-1.107.el6_4.5 will be updated
--> Processing Dependency: glibc-headers = 2.12-1.107.el6_4.5 for package: glibc-devel-2.12-1.107.el6_4.5.x86_64
---> Package kernel-devel.x86_64 0:2.6.32-358.6.2.el6 will be erased
--> Finished Dependency Resolution
Error: Package: glibc-devel-2.12-1.107.el6_4.5.x86_64 (@updates)
           Requires: glibc-headers = 2.12-1.107.el6_4.5
           Removing: glibc-headers-2.12-1.107.el6_4.5.x86_64 (@updates)
               glibc-headers = 2.12-1.107.el6_4.5
           Updated By: glibc-headers-2.12-1.132.el6.x86_64 (base)
               glibc-headers = 2.12-1.132.el6
Error: Package: coreutils-libs-8.4-19.el6_4.2.x86_64 (@updates)
           Requires: coreutils = 8.4-19.el6_4.2
           Removing: coreutils-8.4-19.el6_4.2.x86_64 (@updates)
               coreutils = 8.4-19.el6_4.2
           Updated By: coreutils-8.4-31.el6.x86_64 (base)
               coreutils = 8.4-31.el6
 You could try using --skip-broken to work around the problem
** Found 49 pre-existing rpmdb problem(s), 'yum check' output follows:
ca-certificates-2013.1.94-65.0.el6.noarch is a duplicate with ca-certificates-2010.63-3.el6_1.5.noarch
centos-release-6-5.el6.centos.11.2.x86_64 is a duplicate with centos-release-6-4.el6.centos.10.x86_64
coreutils-libs-8.4-31.el6.x86_64 is a duplicate with coreutils-libs-8.4-19.el6_4.2.x86_64
coreutils-libs-8.4-31.el6.x86_64 has missing requires of coreutils = ('0', '8.4', '31.el6')
cpp-4.4.7-4.el6.x86_64 is a duplicate with cpp-4.4.7-3.el6.x86_64
e2fsprogs-1.41.12-18.el6.x86_64 is a duplicate with e2fsprogs-1.41.12-14.el6_4.4.x86_64
e2fsprogs-libs-1.41.12-18.el6.x86_64 is a duplicate with e2fsprogs-libs-1.41.12-14.el6_4.4.x86_64
gcc-4.4.7-4.el6.x86_64 is a duplicate with gcc-4.4.7-3.el6.x86_64
glib2-2.26.1-3.el6.x86_64 is a duplicate with glib2-2.22.5-7.el6.x86_64
glibc-2.12-1.132.el6.x86_64 is a duplicate with glibc-2.12-1.107.el6_4.5.x86_64
glibc-common-2.12-1.132.el6.x86_64 is a duplicate with glibc-common-2.12-1.107.el6_4.5.x86_64
glibc-devel-2.12-1.132.el6.x86_64 is a duplicate with glibc-devel-2.12-1.107.el6_4.5.x86_64
glibc-devel-2.12-1.132.el6.x86_64 has missing requires of glibc-headers = ('0', '2.12', '1.132.el6')
grep-2.6.3-4.el6.x86_64 is a duplicate with grep-2.6.3-3.el6.x86_64
hwdata-0.233-9.1.el6.noarch is a duplicate with hwdata-0.233-7.9.el6.noarch
kernel-headers-2.6.32-431.el6.x86_64 is a duplicate with kernel-headers-2.6.32-358.23.2.el6.x86_64
libblkid-2.17.2-12.14.el6.x86_64 is a duplicate with libblkid-2.17.2-12.9.el6_4.3.x86_64
libcom_err-1.41.12-18.el6.x86_64 is a duplicate with libcom_err-1.41.12-14.el6_4.4.x86_64
libgcc-4.4.7-4.el6.x86_64 is a duplicate with libgcc-4.4.7-3.el6.x86_64
libgomp-4.4.7-4.el6.x86_64 is a duplicate with libgomp-4.4.7-3.el6.x86_64
libnl-1.1.4-2.el6.x86_64 is a duplicate with libnl-1.1.4-1.el6_4.x86_64
libss-1.41.12-18.el6.x86_64 is a duplicate with libss-1.41.12-14.el6_4.4.x86_64
libstdc++-4.4.7-4.el6.x86_64 is a duplicate with libstdc++-4.4.7-3.el6.x86_64
libstdc++-devel-4.4.7-4.el6.x86_64 is a duplicate with libstdc++-devel-4.4.7-3.el6.x86_64
libuuid-2.17.2-12.14.el6.x86_64 is a duplicate with libuuid-2.17.2-12.9.el6_4.3.x86_64
libxml2-2.7.6-14.el6.x86_64 is a duplicate with libxml2-2.7.6-12.el6_4.1.x86_64
logrotate-3.7.8-17.el6.x86_64 is a duplicate with logrotate-3.7.8-16.el6.x86_64
nspr-4.10.0-1.el6.x86_64 is a duplicate with nspr-4.9.5-2.el6_4.x86_64
nss-3.15.1-15.el6.x86_64 is a duplicate with nss-3.14.3-4.el6_4.x86_64
nss-softokn-3.14.3-9.el6.x86_64 is a duplicate with nss-softokn-3.14.3-3.el6_4.x86_64
nss-softokn-freebl-3.14.3-9.el6.x86_64 is a duplicate with nss-softokn-freebl-3.14.3-3.el6_4.x86_64
nss-sysinit-3.15.1-15.el6.x86_64 is a duplicate with nss-sysinit-3.14.3-4.el6_4.x86_64
nss-util-3.15.1-3.el6.x86_64 is a duplicate with nss-util-3.14.3-3.el6_4.x86_64
openssl-1.0.1e-15.el6.x86_64 is a duplicate with openssl-1.0.0-27.el6_4.2.x86_64
p11-kit-trust-0.18.5-2.el6.x86_64 has installed conflicts nss < ('0', '3.14.3', '33'): nss-3.14.3-4.el6_4.x86_64
pam-1.1.1-17.el6.x86_64 is a duplicate with pam-1.1.1-13.el6.x86_64
4:perl-5.10.1-136.el6.x86_64 is a duplicate with 4:perl-5.10.1-131.el6_4.x86_64
1:perl-Module-Pluggable-3.90-136.el6.x86_64 is a duplicate with 1:perl-Module-Pluggable-3.90-131.el6_4.x86_64
1:perl-Pod-Escapes-1.04-136.el6.x86_64 is a duplicate with 1:perl-Pod-Escapes-1.04-131.el6_4.x86_64
1:perl-Pod-Simple-3.13-136.el6.x86_64 is a duplicate with 1:perl-Pod-Simple-3.13-131.el6_4.x86_64
4:perl-libs-5.10.1-136.el6.x86_64 is a duplicate with 4:perl-libs-5.10.1-131.el6_4.x86_64
3:perl-version-0.77-136.el6.x86_64 is a duplicate with 3:perl-version-0.77-131.el6_4.x86_64
php-common-5.3.3-26.el6.x86_64 is a duplicate with php-common-5.3.3-23.el6_4.x86_64
policycoreutils-2.0.83-19.39.el6.x86_64 is a duplicate with policycoreutils-2.0.83-19.30.el6.x86_64
python-2.6.6-51.el6.x86_64 is a duplicate with python-2.6.6-37.el6_4.x86_64
python-libs-2.6.6-51.el6.x86_64 is a duplicate with python-libs-2.6.6-37.el6_4.x86_64
rpm-4.8.0-37.el6.x86_64 is a duplicate with rpm-4.8.0-32.el6.x86_64
rpm-libs-4.8.0-37.el6.x86_64 is a duplicate with rpm-libs-4.8.0-32.el6.x86_64
sysvinit-tools-2.87-5.dsf.el6.x86_64 is a duplicate with sysvinit-tools-2.87-4.dsf.el6.x86_64
[root@cdn rpm]#
I have tried running yum-complete-transaction and rebuilding the RPM database as per this article:
http://www.cyberciti.biz/tips/rebuildin ... abase.html

Is there any way I can salvage this installation? I need for Yum to somehow start over, identify the currently installed packages and then perform a clean update from 6.4 to 6.5... help!

User avatar
TrevorH
Forum Moderator
Posts: 30575
Joined: 2009/09/24 10:40:56
Location: Brighton, UK

Re: Issues with yum after out of memory error

Post by TrevorH » 2013/12/03 21:46:24

Someone else had a similar problem. One thing you could try is to query

Code: Select all

rpm -qa --qf '%{name}-%{version}.%{release}.%{arch}\n' glibc\*
and see if your i686 and x86_64 versions of each pair of packages match up. If they don't - for example if glibc.x86_64 is version x.y.z and glibc.i686 is x.y.a then you could try yum updating the older one specifically to the same version as the newer one - e.g. `yum update glibc.i686`. Another possibility is that you could try removing the i686 packages if they are not absolutely required on your system. You could also look at package-cleanup --cleandupes
CentOS 6 died in November 2020 - migrate to a new version!
Info for USB installs on http://wiki.centos.org/HowTos/InstallFromUSBkey
CentOS 5 is dead, do not use it.
Full time Geek, part time moderator. Use the FAQ Luke

littleguy
Posts: 2
Joined: 2013/12/03 21:33:35

Re: Issues with yum after out of memory error

Post by littleguy » 2013/12/03 22:17:43

TrevorH wrote:Someone else had a similar problem.
...
Thanks for your reply Trevor! I'm having some small issues.

Here's the output from the command that determines glibc packages:

Code: Select all

[root@cdn ~]# rpm -qa --qf '%{name}-%{version}.%{release}.%{arch}\n' glibc\*
glibc-devel-2.12.1.107.el6_4.5.x86_64
glibc-2.12.1.132.el6.x86_64
glibc-headers-2.12.1.107.el6_4.5.x86_64
glibc-common-2.12.1.107.el6_4.5.x86_64
glibc-common-2.12.1.132.el6.x86_64
glibc-devel-2.12.1.132.el6.x86_64
glibc-2.12.1.107.el6_4.5.x86_64
glibc-2.12.1.107.el6_4.5.i686
I don't know why the i686 package is there... the server is supposed to be x86_64, uname -a says:

Code: Select all

Linux cdn.internal.dev 2.6.32-5-vserver-amd64 #1 SMP Fri May 10 10:52:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
The packages are the same version though...

If I do yum update glibc.i686 I get an error with Multilib..

Code: Select all

[root@cdn ~]# yum update glibc.i686
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: ftp.sunet.se
 * epel: ftp.lysator.liu.se
 * extras: ftp.sunet.se
 * updates: ftp.sunet.se
Setting up Update Process
Resolving Dependencies
--> Running transaction check
---> Package glibc.i686 0:2.12-1.107.el6_4.5 will be updated
---> Package glibc.i686 0:2.12-1.132.el6 will be an update
--> Finished Dependency Resolution
Error:  Multilib version problems found. This often means that the root
       cause is something else and multilib version checking is just
       pointing out that there is a problem. Eg.:

         1. You have an upgrade for glibc which is missing some
            dependency that another package requires. Yum is trying to
            solve this by installing an older version of glibc of the
            different architecture. If you exclude the bad architecture
            yum will tell you what the root cause is (which package
            requires what). You can try redoing the upgrade with
            --exclude glibc.otherarch ... this should give you an error
            message showing the root cause of the problem.

         2. You have multiple architectures of glibc installed, but
            yum can only see an upgrade for one of those arcitectures.
            If you don't want/need both architectures anymore then you
            can remove the one with the missing update and everything
            will work.

         3. You have duplicate versions of glibc installed already.
            You can use "yum check" to get yum show these errors.

       ...you can also use --setopt=protected_multilib=false to remove
       this checking, however this is almost never the correct thing to
       do as something else is very likely to go wrong (often causing
       much more problems).

       Protected multilib versions: glibc-2.12-1.132.el6.i686 != glibc-2.12-1.107.el6_4.5.x86_64
 You could try using --skip-broken to work around the problem
** Found 49 pre-existing rpmdb problem(s), 'yum check' output follows:
ca-certificates-2013.1.94-65.0.el6.noarch is a duplicate with ca-certificates-2010.63-3.el6_1.5.noarch
centos-release-6-5.el6.centos.11.2.x86_64 is a duplicate with centos-release-6-4.el6.centos.10.x86_64
coreutils-libs-8.4-31.el6.x86_64 is a duplicate with coreutils-libs-8.4-19.el6_4.2.x86_64
coreutils-libs-8.4-31.el6.x86_64 has missing requires of coreutils = ('0', '8.4', '31.el6')
cpp-4.4.7-4.el6.x86_64 is a duplicate with cpp-4.4.7-3.el6.x86_64
e2fsprogs-1.41.12-18.el6.x86_64 is a duplicate with e2fsprogs-1.41.12-14.el6_4.4.x86_64
e2fsprogs-libs-1.41.12-18.el6.x86_64 is a duplicate with e2fsprogs-libs-1.41.12-14.el6_4.4.x86_64
gcc-4.4.7-4.el6.x86_64 is a duplicate with gcc-4.4.7-3.el6.x86_64
glib2-2.26.1-3.el6.x86_64 is a duplicate with glib2-2.22.5-7.el6.x86_64
glibc-2.12-1.132.el6.x86_64 is a duplicate with glibc-2.12-1.107.el6_4.5.x86_64
glibc-common-2.12-1.132.el6.x86_64 is a duplicate with glibc-common-2.12-1.107.el6_4.5.x86_64
glibc-devel-2.12-1.132.el6.x86_64 is a duplicate with glibc-devel-2.12-1.107.el6_4.5.x86_64
glibc-devel-2.12-1.132.el6.x86_64 has missing requires of glibc-headers = ('0', '2.12', '1.132.el6')
grep-2.6.3-4.el6.x86_64 is a duplicate with grep-2.6.3-3.el6.x86_64
hwdata-0.233-9.1.el6.noarch is a duplicate with hwdata-0.233-7.9.el6.noarch
kernel-headers-2.6.32-431.el6.x86_64 is a duplicate with kernel-headers-2.6.32-358.23.2.el6.x86_64
libblkid-2.17.2-12.14.el6.x86_64 is a duplicate with libblkid-2.17.2-12.9.el6_4.3.x86_64
libcom_err-1.41.12-18.el6.x86_64 is a duplicate with libcom_err-1.41.12-14.el6_4.4.x86_64
libgcc-4.4.7-4.el6.x86_64 is a duplicate with libgcc-4.4.7-3.el6.x86_64
libgomp-4.4.7-4.el6.x86_64 is a duplicate with libgomp-4.4.7-3.el6.x86_64
libnl-1.1.4-2.el6.x86_64 is a duplicate with libnl-1.1.4-1.el6_4.x86_64
libss-1.41.12-18.el6.x86_64 is a duplicate with libss-1.41.12-14.el6_4.4.x86_64
libstdc++-4.4.7-4.el6.x86_64 is a duplicate with libstdc++-4.4.7-3.el6.x86_64
libstdc++-devel-4.4.7-4.el6.x86_64 is a duplicate with libstdc++-devel-4.4.7-3.el6.x86_64
libuuid-2.17.2-12.14.el6.x86_64 is a duplicate with libuuid-2.17.2-12.9.el6_4.3.x86_64
libxml2-2.7.6-14.el6.x86_64 is a duplicate with libxml2-2.7.6-12.el6_4.1.x86_64
logrotate-3.7.8-17.el6.x86_64 is a duplicate with logrotate-3.7.8-16.el6.x86_64
nspr-4.10.0-1.el6.x86_64 is a duplicate with nspr-4.9.5-2.el6_4.x86_64
nss-3.15.1-15.el6.x86_64 is a duplicate with nss-3.14.3-4.el6_4.x86_64
nss-softokn-3.14.3-9.el6.x86_64 is a duplicate with nss-softokn-3.14.3-3.el6_4.x86_64
nss-softokn-freebl-3.14.3-9.el6.x86_64 is a duplicate with nss-softokn-freebl-3.14.3-3.el6_4.x86_64
nss-sysinit-3.15.1-15.el6.x86_64 is a duplicate with nss-sysinit-3.14.3-4.el6_4.x86_64
nss-util-3.15.1-3.el6.x86_64 is a duplicate with nss-util-3.14.3-3.el6_4.x86_64
openssl-1.0.1e-15.el6.x86_64 is a duplicate with openssl-1.0.0-27.el6_4.2.x86_64
p11-kit-trust-0.18.5-2.el6.x86_64 has installed conflicts nss < ('0', '3.14.3', '33'): nss-3.14.3-4.el6_4.x86_64
pam-1.1.1-17.el6.x86_64 is a duplicate with pam-1.1.1-13.el6.x86_64
4:perl-5.10.1-136.el6.x86_64 is a duplicate with 4:perl-5.10.1-131.el6_4.x86_64
1:perl-Module-Pluggable-3.90-136.el6.x86_64 is a duplicate with 1:perl-Module-Pluggable-3.90-131.el6_4.x86_64
1:perl-Pod-Escapes-1.04-136.el6.x86_64 is a duplicate with 1:perl-Pod-Escapes-1.04-131.el6_4.x86_64
1:perl-Pod-Simple-3.13-136.el6.x86_64 is a duplicate with 1:perl-Pod-Simple-3.13-131.el6_4.x86_64
4:perl-libs-5.10.1-136.el6.x86_64 is a duplicate with 4:perl-libs-5.10.1-131.el6_4.x86_64
3:perl-version-0.77-136.el6.x86_64 is a duplicate with 3:perl-version-0.77-131.el6_4.x86_64
php-common-5.3.3-26.el6.x86_64 is a duplicate with php-common-5.3.3-23.el6_4.x86_64
policycoreutils-2.0.83-19.39.el6.x86_64 is a duplicate with policycoreutils-2.0.83-19.30.el6.x86_64
python-2.6.6-51.el6.x86_64 is a duplicate with python-2.6.6-37.el6_4.x86_64
python-libs-2.6.6-51.el6.x86_64 is a duplicate with python-libs-2.6.6-37.el6_4.x86_64
rpm-4.8.0-37.el6.x86_64 is a duplicate with rpm-4.8.0-32.el6.x86_64
rpm-libs-4.8.0-37.el6.x86_64 is a duplicate with rpm-libs-4.8.0-32.el6.x86_64
sysvinit-tools-2.87-5.dsf.el6.x86_64 is a duplicate with sysvinit-tools-2.87-4.dsf.el6.x86_64
At the end of each yum output, there's a bunch of "X is a duplicate with Y" errors. Can you clear that conflict somehow?

Also, could you advise on how to remove the i686 package?

Thanks again!

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TrevorH
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Re: Issues with yum after out of memory error

Post by TrevorH » 2013/12/03 22:34:55

The easy question is the one about why is the i686 package there and the answer is that is the 32 bit glibc and is probably pulled in by another 32 bit package that you installed. The real problem is that you have duplicate packages with different version numbers and that's what's confusing things. For example you have glibc.x86_64 2.12.1.132.el6 and 2.12.1.107.el6_4.5 and the same mix with glibc-common and glibc-devel.

Getting out of this is not going to be easy and I would make sure that anything on this server that you really need is backed up and safe before you start doing anything about this. Personally I think I would start by removing the packages that are not essential to the operation of the server that are coming up as duplicated - so glibc-headers, kernel-devel, gcc, cpp - that looks about it. I think I'd then try a `yum reinstall glibc-2.12.1.132.el6.x86_64 glibc-common-2.12.1.132.el6.x86_64` and see if that helps at all.

Backup first before you try anything!
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Info for USB installs on http://wiki.centos.org/HowTos/InstallFromUSBkey
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Blacktiger
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Location: Netherlands

Re: Issues with yum after out of memory error

Post by Blacktiger » 2013/12/06 16:52:19

Sorry to break in to this problem. I did not have a memory error, but have the exactly the same problem after updating from 6.4 to 6.5 last night.

After rebooting the server, because a kernel update was also present, the server did not respond anymore due to a kernel panic.
So the datacenter switched to the previous kernel and the server rebooted again, but then when updating glibc.i686 exactly the same problem occured with exactly the same error notices (and version numbers).

Strangely enough, we got 2 other servers, same way installed, without any problems. And both have glibc.i686 installed too, because some application we run on it need the 32bit glibc.

The command:
yum reinstall glibc-2.12.1.132.el6.x86_64 glibc-common-2.12.1.132.el6.x86_64
Only gave this output:
No Match for argument: glibc-2.12.1.132.el6.x86_64
No Match for argument: glibc-common-2.12.1.132.el6.x86_64
Error: Nothing to do
Any help is greatly appreciated.

max_xxv
Posts: 9
Joined: 2014/05/02 07:40:31

Re: Issues with yum after out of memory error

Post by max_xxv » 2014/05/02 08:18:36

Hi! I've the same problem in a VPS ( OVH ) server:

Code: Select all

rpm -qa --qf '%{name}-%{version}.%{release}.%{arch}\n' glibc\*
glibc-2.12.1.132.el6.x86_64
glibc-headers-2.12.1.132.el6.x86_64
glibc-common-2.12.1.132.el6.x86_64
glibc-devel-2.12.1.132.el6.x86_64
glibc-2.12.1.132.el6.i686
and command like pgrep fail:

Code: Select all

pgrep: error while loading shared libraries: libproc-3.2.8.so: wrong ELF class: ELFCLASS32
Someone can help me?

Best regards
Mauro Soligo ( Italy )

Blacktiger
Posts: 5
Joined: 2005/09/20 23:12:23
Location: Netherlands

Re: Issues with yum after out of memory error

Post by Blacktiger » 2014/05/02 12:16:27

Well, nobody gave me a solution here.
But for future references... you could try this solution, it helped me with my problem that time.

Issue the following commands as root user.
1.) yum install yum-utils
2.) yum-complete-transaction
3.) yum clean metadata
4.) yum clean all
5.) package-cleanup --dupes (check if only the doubles are in the list)
6.) package-cleanup --cleandupes
7.) yum check (and see if it stops without issues).

Hope it will work for you too.

max_xxv
Posts: 9
Joined: 2014/05/02 07:40:31

Re: Issues with yum after out of memory error

Post by max_xxv » 2014/05/02 12:23:42

I've used all command but at last step:

Code: Select all

yum check
Loaded plugins: fastestmirror
coreutils-8.4-19.el6_4.2.x86_64 has missing requires of coreutils-libs = ('0', '8.4', '19.el6_4.2')
coreutils-libs-8.4-31.el6_5.1.x86_64 has missing requires of coreutils = ('0', '8.4', '31.el6_5.1')
Error: check all

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TrevorH
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Re: Issues with yum after out of memory error

Post by TrevorH » 2014/05/02 12:33:48

Post the output of rpm -qa coreutils\*
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max_xxv
Posts: 9
Joined: 2014/05/02 07:40:31

Re: Issues with yum after out of memory error

Post by max_xxv » 2014/05/02 12:39:32

rpm -qa coreutils\*
coreutils-libs-8.4-31.el6_5.1.x86_64
coreutils-8.4-19.el6_4.2.x86_64

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