Errors when trying to update mySQL

argosmedia · **Posted:** Wed May 30, 2012 9:46 am

I tried to update mySQL but I see a lot of errors in the end. Is this normal, or is something broken? If so, what should I do? The 2 recommendations at the end didn't do anything. MySQL is not yet updated.

Code:

 yum upgrade mysql
Loaded plugins: fastestmirror, presto, priorities
Loading mirror speeds from cached hostfile
 * atomic: www7.atomicorp.com
 * base: mirrors.supportex.net
 * extras: mirrors.supportex.net
 * updates: mirror.yourwebhoster.eu
235 packages excluded due to repository priority protections
Setting up Upgrade Process
Resolving Dependencies
--> Running transaction check
---> Package mysql.x86_64 0:5.1.61-1.el6_2.1 will be updated
--> Processing Dependency: mysql = 5.1.61-1.el6_2.1 for package: mysql-server-5.1.61-1.el6_2.1.x86_64
---> Package mysql.x86_64 0:5.5.24-6.el6.art will be an update
--> Processing Dependency: mysql-libs(x86-64) = 5.5.24-6.el6.art for package: mysql-5.5.24-6.el6.art.x86_64
--> Running transaction check
---> Package mysql-libs.x86_64 0:5.1.61-1.el6_2.1 will be updated
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: perl-DBD-MySQL-4.013-3.el6.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: psa-libpam-plesk-10.13.4-cos6.build1013111102.18.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: plesk-mail-qc-driver-10.13.4-cos6.build1013111102.18.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: php-mysql-5.3.13-5.el6.art.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: ossec-hids-server-2.6-10.el6.art.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: psa-backup-manager-10.13.4-cos6.build1013111102.18.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: asl-php-mysql-5.4.3-3.el6.art.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: psa-spamassassin-10.13.4-cos6.build1013111102.18.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: plesk-core-10.13.4-cos6.build1013111102.18.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: psa-mail-driver-common-10.13.4-cos6.build1013111102.18.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: roadsend-php-libs-2.9.8-10.2.el6.art.x86_64
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: asl-php-mysql-5.4.3-3.el6.art.x86_64
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: php-mysql-5.3.13-5.el6.art.x86_64
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: perl-DBD-MySQL-4.013-3.el6.x86_64
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: ossec-hids-server-2.6-10.el6.art.x86_64
--> Processing Dependency: libmysqlclient_r.so.16()(64bit) for package: mysql-connector-odbc-5.1.5r1144-7.el6.x86_64
--> Processing Dependency: libmysqlclient_r.so.16()(64bit) for package: asl-php-mysql-5.4.3-3.el6.art.x86_64
--> Processing Dependency: libmysqlclient_r.so.16(libmysqlclient_16)(64bit) for package: mysql-connector-odbc-5.1.5r1144-7.el6.x86_64
--> Processing Dependency: libmysqlclient_r.so.16(libmysqlclient_16)(64bit) for package: asl-php-mysql-5.4.3-3.el6.art.x86_64
---> Package mysql-libs.x86_64 0:5.5.24-6.el6.art will be an update
---> Package mysql-server.x86_64 0:5.1.61-1.el6_2.1 will be updated
---> Package mysql-server.x86_64 0:5.5.24-6.el6.art will be an update
--> Running transaction check
---> Package mysqlclient16.x86_64 0:5.1.59-2.el6.art will be installed
asl-3.0/filelists_db                                     | 1.7 MB     00:03
atomic/filelists_db                                      | 514 kB     00:00
http://www7.atomicorp.com/channels/atomic/centos/6/x86_64/repodata/filelists.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
atomic/filelists_db                                      | 514 kB     00:01
http://www6.atomicorp.com/channels/atomic/centos/6/x86_64/repodata/filelists.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
atomic/filelists_db                                      | 514 kB     00:01
http://www5.atomicorp.com/channels/atomic/centos/6/x86_64/repodata/filelists.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
atomic/filelists_db                                      | 514 kB     00:01
http://www3.atomicorp.com/channels/atomic/centos/6/x86_64/repodata/filelists.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
atomic/filelists_db                                      | 514 kB     00:01
http://www2.atomicorp.com/channels/atomic/centos/6/x86_64/repodata/filelists.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
atomic/filelists_db                                      | 514 kB     00:01
http://www4.atomicorp.com/channels/atomic/centos/6/x86_64/repodata/filelists.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
Error: failure: repodata/filelists.sqlite.bz2 from atomic: [Errno 256] No more mirrors to try.
 You could try using --skip-broken to work around the problem
 You could try running: rpm -Va --nofiles --nodigest

scott · **Posted:** Wed May 30, 2012 10:03 am

Clean your yum data, its out of date

argosmedia · **Posted:** Wed May 30, 2012 10:24 am

Ah, looked that up in Google and found what command to use and how to update not only mySQl but also the rest of the components. Now it's up to date again. Thanks!
===========

EDIT:
Oops, I was too quick. Although there were no errors and the update seemed to go fine, the reported version in phpinfo is still 5.1.59, instead of 5.5. And ASL reports: "Critical Risk: Un-Applied updates for your system were detected. A full list of available updates is available in /var/asl/data/updates_pending.log." That file has this content:

Code:

libc-client.x86_64                   2007e-11.el6.art                    atomic 
libedit.x86_64                       3.0-2.20090923cvs.el6.art           atomic 
lldpad.x86_64                        0.9.43-13.el6_2                     updates
mysql.x86_64                         5.5.24-6.el6.art                    atomic 
mysql-libs.x86_64                    5.5.24-6.el6.art                    atomic 
mysql-server.x86_64                  5.5.24-6.el6.art                    atomic 
openssl.x86_64                       1.0.0-20.el6_2.5                    updates
perl-IO-Socket-INET6.noarch          2.67-1.el6.art                      atomic 
sqlite.x86_64                        3.7.9-1.el6.art                     atomic 
tzdata.noarch                        2012c-1.el6                         updates

I have a feeling I'm doing something wrong... I ran the commands yum clean all, and yum update all (or something like that, I closed Putty and Google again). And then restarted httpd and mysql. Isn't that correct? How do I have ASL and Plesk make sure I always have an updated system?

breun · **Posted:** Wed May 30, 2012 5:23 pm

argosmedia wrote:

I have a feeling I'm doing something wrong... I ran the commands yum clean all, and yum update all (or something like that, I closed Putty and Google again). And then restarted httpd and mysql. Isn't that correct?

Can you show us what MySQL packages you have installed?

Code:

rpm -qa | grep -i mysql

By the way, it's not necessary to restart Apache httpd when upgrading MySQL, but if you also updated other software then that might have made sense (for mod_php for instance it does).

argosmedia wrote:

How do I have ASL and Plesk make sure I always have an updated system?

I'm sorry to tell you it's not yet possible to completely automate system administration. It still takes a skilled admin to take good care of a server. At least you'll need to run the Plesk updater frequently and you can use yum for everything else as long as you stick with RPM packages from configured yum repositories for the rest of the software on your server. You could run yum via cron (or yum-updatesd?), but I'd advise against it. I at least want to be there when stuff gets changed and you'll also sometimes need to take care of updating/merging configuration files when updating packages for instance.

argosmedia · **Posted:** Wed May 30, 2012 5:30 pm

Thanks for your reply. This is the output of the command:

Code:

[root@vps ~]# rpm -qa | grep -i mysql
php-mysql-5.3.13-5.el6.art.x86_64
mysqlclient16-5.1.59-2.el6.art.x86_64
asl-php-mysql-5.4.3-3.el6.art.x86_64
mysqltuner-1.2.0-1.el6.art.noarch
mysql-libs-5.5.24-6.el6.art.x86_64
mysql-server-5.5.24-6.el6.art.x86_64
mysql-connector-odbc-5.1.5r1144-7.el6.x86_64
perl-DBD-MySQL-4.013-3.el6.x86_64
mysql-5.5.24-6.el6.art.x86_64

LOL, I'm far from skilled yet. Much to learn still!

breun · **Posted:** Wed May 30, 2012 5:45 pm

Ok, so apparently you have installed the MySQL 5.5.24 packages. The ART mysql-server package is configured to restart automatically after installation, so you should be running 5.5.24 now. What is the output of the following command?

Code:

mysqladmin -uadmin -p`cat /etc/psa/.psa.shadow` version

argosmedia · **Posted:** Wed May 30, 2012 5:54 pm

breun wrote:

Ok, so apparently you have installed the MySQL 5.5.24 packages. The ART mysql-server package is configured to restart automatically after installation, so you should be running 5.5.24 now. What is the output of the following command?

Code:

mysqladmin -uadmin -p`cat /etc/psa/.psa.shadow` version

Really? That sounds good. The command gives:

Code:

mysqladmin  Ver 8.42 Distrib 5.5.24, for Linux on x86_64
Copyright (c) 2000, 2011, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Server version          5.5.24-cll
Protocol version        10
Connection              Localhost via UNIX socket
UNIX socket             /var/lib/mysql/mysql.sock
Uptime:                 7 hours 22 min 25 sec

Threads: 2  Questions: 210642  Slow queries: 7636  Opens: 995  Flush tables: 1  Open tables: 436  Queries per second avg: 7.935

However, the info.php from a domain on the server says it's version "5.1.59". And Plesk > Tools & Settings > Server Components say it's version "5.1.61-1.el6_2.1".

breun · **Posted:** Fri Jun 01, 2012 3:49 pm

argosmedia wrote:

Code:

mysqladmin  Ver 8.42 Distrib 5.5.24, for Linux on x86_64
Copyright (c) 2000, 2011, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Server version          5.5.24-cll
Protocol version        10
Connection              Localhost via UNIX socket
UNIX socket             /var/lib/mysql/mysql.sock
Uptime:                 7 hours 22 min 25 sec

Threads: 2  Questions: 210642  Slow queries: 7636  Opens: 995  Flush tables: 1  Open tables: 436  Queries per second avg: 7.935

Ok, so you really are running MySQL 5.5.24.

argosmedia wrote:

However, the info.php from a domain on the server says it's version "5.1.59".

CentOS 6 comes with MySQL 5.1 by default, so that's the version of the MySQL client library that all CentOS 6 RPM packages depend on. For this reason the ART MySQL packages install the MySQL 5.1 client library on CentOS 6. This is why you have mysqlclient16-5.1.59-2.el6.art.x86_64 installed.

You could recompile PHP against MySQL 5.5, but because of the compatibility package you don't need to and I'd recommend being happy about that. Rest assured that your MySQL server is version 5.5.

argosmedia wrote:

And Plesk > Tools & Settings > Server Components say it's version "5.1.61-1.el6_2.1".

CentOS 6 currently ships MySQL 5.1.61. I guess this is stale information that was not up-to-date when you viewed it. Plesk might not update this info in realtime, maybe only daily or something. Does Plesk still say MySQL 5.1.61 is installed?

Errors when trying to update mySQL

Who is online