Centos 6 install atomic repo mysql upgrade prob

[ccisadmin]

Building a new Centos Plesk11 server like this:

Install Centos 6.3 64bit from DVD ISO
yum update
Install latest Plesk 11 + microupdates using autoinstaller
Install ASL 3 wget -q -O - https://www.atomicorp.com/installers/asl |sh
Edit grub, disable ASL kernel (Since im using Hyper-V 3, cant get integration components working)
reboot
Add atomic repo: wget -q -O - http://www.atomicorp.com/installers/atomic | sh

Now problem with yum update and mysql:

[root@Plesk-C64 etc]# yum update
Loaded plugins: fastestmirror
Determining fastest mirrors
* asl-3.0: www5.atomicorp.com
* atomic: www5.atomicorp.com
* base: mirror.its.sfu.ca
* extras: mirror.its.sfu.ca
* updates: mirror.its.sfu.ca
asl-3.0 | 1.9 kB 00:00
asl-3.0/primary_db | 297 kB 00:02
atomic | 1.9 kB 00:00
atomic/primary_db | 406 kB 00:02
base | 3.7 kB 00:00
base/primary_db | 4.5 MB 00:24
extras | 3.5 kB 00:00
extras/primary_db | 23 kB 00:00
updates | 3.5 kB 00:00
updates/primary_db | 5.1 MB 00:22
Setting up Update Process
Resolving Dependencies
--> Running transaction check
---> Package libc-client.x86_64 0:2007e-11.el6 will be updated
---> Package libc-client.x86_64 0:2007e-11.el6.art will be an update
---> Package libedit.x86_64 0:2.11-4.20080712cvs.1.el6 will be updated
---> Package libedit.x86_64 0:3.0-2.20090923cvs.el6.art will be an update
---> Package mysql.x86_64 0:5.1.67-1.el6_3 will be updated
---> Package mysql.x86_64 0:5.5.30-15.el6.art will be an update
---> Package mysql-libs.x86_64 0:5.1.67-1.el6_3 will be updated
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: psa-mail-driver-common-11.0.9-cos6.build110120608.16.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: psa-backup-manager-11.0.9-cos6.build110120608.16.x86_64
--> 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-fileserver-11.0.9-cos6.build110120608.16.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: plesk-core-11.0.9-cos6.build110120608.16.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: psa-libpam-plesk-11.0.9-cos6.build110120608.16.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: php-mysql-5.3.21-14.el6.art.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: 2:postfix-2.6.6-2.2.el6_1.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: plesk-mail-qc-driver-11.0.9-cos6.build110120608.16.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: php-mysql-5.3.21-14.el6.art.x86_64
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: 2:postfix-2.6.6-2.2.el6_1.x86_64
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: perl-DBD-MySQL-4.013-3.el6.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(libmysqlclient_16)(64bit) for package: mysql-connector-odbc-5.1.5r1144-7.el6.x86_64
---> Package mysql-libs.x86_64 0:5.5.30-15.el6.art will be an update
---> Package mysql-server.x86_64 0:5.1.67-1.el6_3 will be updated
---> Package mysql-server.x86_64 0:5.5.30-15.el6.art will be an update
--> Processing Dependency: libaio.so.1(LIBAIO_0.4)(64bit) for package: mysql-server-5.5.30-15.el6.art.x86_64
--> Processing Dependency: libaio.so.1(LIBAIO_0.1)(64bit) for package: mysql-server-5.5.30-15.el6.art.x86_64
--> Processing Dependency: libaio.so.1()(64bit) for package: mysql-server-5.5.30-15.el6.art.x86_64
---> Package php.x86_64 0:5.3.3-14.el6_3 will be updated
---> Package php.x86_64 0:5.3.21-14.el6.art will be an update
---> Package php-cli.x86_64 0:5.3.3-14.el6_3 will be updated
---> Package php-cli.x86_64 0:5.3.21-14.el6.art will be an update
---> Package php-common.x86_64 0:5.3.3-14.el6_3 will be updated
---> Package php-common.x86_64 0:5.3.21-14.el6.art will be an update
---> Package php-gd.x86_64 0:5.3.3-14.el6_3 will be updated
---> Package php-gd.x86_64 0:5.3.21-14.el6.art will be an update
---> Package php-imap.x86_64 0:5.3.3-14.el6_3 will be updated
---> Package php-imap.x86_64 0:5.3.21-14.el6.art will be an update
---> Package php-ioncube-loader.x86_64 1:4.2.2-2.el6.art will be obsoleting
--> Processing Dependency: php-devel for package: 1:php-ioncube-loader-4.2.2-2.el6.art.x86_64
---> Package php-mbstring.x86_64 0:5.3.3-14.el6_3 will be updated
---> Package php-mbstring.x86_64 0:5.3.21-14.el6.art will be an update
---> Package php-mysql.x86_64 0:5.3.3-14.el6_3 will be updated
---> Package php-mysql.x86_64 0:5.3.21-14.el6.art will be an update
---> Package php-pdo.x86_64 0:5.3.3-14.el6_3 will be updated
---> Package php-pdo.x86_64 0:5.3.21-14.el6.art will be an update
---> Package php-xml.x86_64 0:5.3.3-14.el6_3 will be updated
---> Package php-xml.x86_64 0:5.3.21-14.el6.art will be an update
---> Package php5-ioncube-loader.x86_64 0:4.0.14-12042719 will be obsoleted
---> Package psa-atmail.noarch 1:1.05-cos6.build110120606.19 will be updated
---> Package psa-atmail.noarch 1:1.05-5.el6.art will be an update
--> Processing Dependency: perl(CGI) for package: 1:psa-atmail-1.05-5.el6.art.noarch
---> Package sqlite.x86_64 0:3.6.20-1.el6 will be updated
---> Package sqlite.x86_64 0:3.7.9-1.el6.art will be an update
--> Running transaction check
---> Package libaio.x86_64 0:0.3.107-10.el6 will be installed
---> Package mysqlclient16.x86_64 0:5.1.59-2.el6.art will be installed
---> Package perl-CGI.x86_64 0:3.51-127.el6 will be installed
---> Package php-devel.x86_64 0:5.3.21-14.el6.art will be installed
--> Processing Dependency: autoconf for package: php-devel-5.3.21-14.el6.art.x86_64
--> Processing Dependency: automake for package: php-devel-5.3.21-14.el6.art.x86_64
--> Running transaction check
---> Package autoconf.noarch 0:2.63-5.1.el6 will be installed
---> Package automake.noarch 0:1.11.1-1.2.el6 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

===========================================================================================================================================================================================================================================
Package Arch Version Repository Size
===========================================================================================================================================================================================================================================
Installing:
php-ioncube-loader x86_64 1:4.2.2-2.el6.art atomic 1.2 M
replacing php5-ioncube-loader.x86_64 4.0.14-12042719
Updating:
libc-client x86_64 2007e-11.el6.art atomic 513 k
libedit x86_64 3.0-2.20090923cvs.el6.art atomic 74 k
mysql x86_64 5.5.30-15.el6.art atomic 5.7 M
mysql-libs x86_64 5.5.30-15.el6.art atomic 766 k
mysql-server x86_64 5.5.30-15.el6.art atomic 10 M
php x86_64 5.3.21-14.el6.art atomic 2.4 M
php-cli x86_64 5.3.21-14.el6.art atomic 2.3 M
php-common x86_64 5.3.21-14.el6.art atomic 900 k
php-gd x86_64 5.3.21-14.el6.art atomic 132 k
php-imap x86_64 5.3.21-14.el6.art atomic 68 k
php-mbstring x86_64 5.3.21-14.el6.art atomic 895 k
php-mysql x86_64 5.3.21-14.el6.art atomic 80 k
php-pdo x86_64 5.3.21-14.el6.art atomic 108 k
php-xml x86_64 5.3.21-14.el6.art atomic 159 k
psa-atmail noarch 1:1.05-5.el6.art atomic 2.8 M
sqlite x86_64 3.7.9-1.el6.art atomic 348 k
Installing for dependencies:
autoconf noarch 2.63-5.1.el6 base 781 k
automake noarch 1.11.1-1.2.el6 base 550 k
libaio x86_64 0.3.107-10.el6 base 21 k
mysqlclient16 x86_64 5.1.59-2.el6.art asl-3.0 1.4 M
perl-CGI x86_64 3.51-127.el6 base 207 k
php-devel x86_64 5.3.21-14.el6.art atomic 1.1 M

Transaction Summary
===========================================================================================================================================================================================================================================
Install 7 Package(s)
Upgrade 16 Package(s)

Total download size: 32 M
Is this ok [y/N]: y
Downloading Packages:
(1/23): autoconf-2.63-5.1.el6.noarch.rpm | 781 kB 00:04
(2/23): automake-1.11.1-1.2.el6.noarch.rpm | 550 kB 00:02
(3/23): libaio-0.3.107-10.el6.x86_64.rpm | 21 kB 00:00
(4/23): libc-client-2007e-11.el6.art.x86_64.rpm | 513 kB 00:05
(5/23): libedit-3.0-2.20090923cvs.el6.art.x86_64.rpm | 74 kB 00:00
(6/23): mysql-5.5.30-15.el6.art.x86_64.rpm | 5.7 MB 00:45
(7/23): mysql-libs-5.5.30-15.el6.art.x86_64.rpm | 766 kB 00:04
(8/23): mysql-server-5.5.30-15.el6.art.x86_64.rpm | 10 MB 01:33
(9/23): mysqlclient16-5.1.59-2.el6.art.x86_64.rpm | 1.4 MB 00:13
(10/23): perl-CGI-3.51-127.el6.x86_64.rpm | 207 kB 00:01
(11/23): php-5.3.21-14.el6.art.x86_64.rpm | 2.4 MB 00:20
(12/23): php-cli-5.3.21-14.el6.art.x86_64.rpm | 2.3 MB 00:20
(13/23): php-common-5.3.21-14.el6.art.x86_64.rpm | 900 kB 00:07
(14/23): php-devel-5.3.21-14.el6.art.x86_64.rpm | 1.1 MB 00:07
(15/23): php-gd-5.3.21-14.el6.art.x86_64.rpm | 132 kB 00:01
(16/23): php-imap-5.3.21-14.el6.art.x86_64.rpm | 68 kB 00:00
(17/23): php-ioncube-loader-4.2.2-2.el6.art.x86_64.rpm | 1.2 MB 00:11
(18/23): php-mbstring-5.3.21-14.el6.art.x86_64.rpm | 895 kB 00:04
(19/23): php-mysql-5.3.21-14.el6.art.x86_64.rpm | 80 kB 00:00
(20/23): php-pdo-5.3.21-14.el6.art.x86_64.rpm | 108 kB 00:00
(21/23): php-xml-5.3.21-14.el6.art.x86_64.rpm | 159 kB 00:00
(22/23): psa-atmail-1.05-5.el6.art.noarch.rpm | 2.8 MB 00:20
(23/23): sqlite-3.7.9-1.el6.art.x86_64.rpm | 348 kB 00:01
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 121 kB/s | 32 MB 04:34
Running rpm_check_debug
Running Transaction Test


Transaction Check Error:
file /usr/lib64/mysql/libmysqlclient.so.18.0.0 from install of mysql-libs-5.5.30-15.el6.art.x86_64 conflicts with file from package mysqlclient18-5.5.28-6.el6.art.x86_64

[root@Plesk-C64 etc]# rpm -qa |grep mysql
mysql-server-5.1.67-1.el6_3.x86_64
mysql-connector-odbc-5.1.5r1144-7.el6.x86_64
mysql-5.1.67-1.el6_3.x86_64
php-mysql-5.3.3-14.el6_3.x86_64
asl-php-mysqlnd-5.4.11-11.el6.art.x86_64
mysqltuner-1.2.0-5.el6.art.noarch
mysqlclient18-5.5.28-6.el6.art.x86_64
mysql-libs-5.1.67-1.el6_3.x86_64
[root@Plesk-C64 etc]#

Any hints how I can get past this?

[breun]

Remove mysqlclient18 and try again. Would be nice if mysql-libs 5.5.x would obsolete mysqlclient18 so yum would be able to resolve this automatically.

[scott]

Obsoletes would mean that mysqlclient18 is always replaced by mysql-libs, and therefore you could never have a client-only library

[breun]

Obsoletes would mean that mysqlclient18 is always replaced by mysql-libs, and therefore you could never have a client-only library

I understand, but is that a problem? The mysql-libs package contains libmysqlclient.so.18.

[scott]

thats the sticky wicket so to speak, the mysql-libs packages cant live togther (ie 5.1 and 5.5) because they use the same name, so one is treated like an upgrade over the other. To get around that, you use a different name (mysqlclient18) and then end up in an alternate condition where the two packages overlap, and wont allow an upgrade. So then you could try putting the mysql library in a different directory, which also doesnt work because the order that mysql libraries are found causes ldconfig to create an error condition where it will link a _r.so in place and that in turn overrides all the other mysql libraries.

[breun]

thats the sticky wicket so to speak, the mysql-libs packages cant live togther (ie 5.1 and 5.5) because they use the same name, so one is treated like an upgrade over the other. To get around that, you use a different name (mysqlclient18) and then end up in an alternate condition where the two packages overlap, and wont allow an upgrade.

Say, I have installed MySQL from CentOS 6 which comes with a mysql-libs-5.1.67 package, which contains libmysqlclient.so.16. I could install mysqlclient18 from Atomic for any applications that require libmysqlclient.so.18. Say I then want to upgrade to MySQL 5.5 from Atomic. The Atomic mysql-libs-5.5.30 package also contains libmysqlclient.so.18, so that's why I'd get a conflict like reported in this thread. I was thinking the mysql-libs-5.5.30 package could obsolete the mysqlclient18 package to allow for this upgrade. Is that correct? Or am I missing something else?

[scott]

Using your example, If you tagged mysql-libs-5.5.30 with Obsoletes: mysqlclient18 its going to do exactly what you told it to. Meaning mysqlclient18 will be upgraded over with mysql-libs-5.5.30. Which means that mysql-libs-5.1.67 would also be upgraded by mysql-libs-5.5.30 ( %{name} is identical on both packages). And since mysql-server-5.1.67 Requires: on mysql-libs-5.1.67, this too would be upgraded to mysql-server 5.5.30 since the mysql-libs-5.1.67 package is no longer installed. Ultimately this would disallow the condition of having a mysql 5.1 server, with both mysql 5.1 and 5.5 libraries.

[ccisadmin]

Thanks for all the replies. If I try to remove mysqlclient18:

[root@Plesk-C64 ~]# yum erase mysqlclient18
Loaded plugins: fastestmirror
Setting up Remove Process
Resolving Dependencies
--> Running transaction check
---> Package mysqlclient18.x86_64 0:5.5.28-6.el6.art will be erased
--> Processing Dependency: libmysqlclient.so.18()(64bit) for package: ossec-hids-server-2.7-20.el6.art.x86_64
--> Processing Dependency: libmysqlclient.so.18(libmysqlclient_16)(64bit) for package: ossec-hids-server-2.7-20.el6.art.x86_64
--> Running transaction check
---> Package ossec-hids-server.x86_64 0:2.7-20.el6.art will be erased
--> Finished Dependency Resolution

Dependencies Resolved

===========================================================================================================================================================================================================================================
Package Arch Version Repository Size
===========================================================================================================================================================================================================================================
Removing:
mysqlclient18 x86_64 5.5.28-6.el6.art @asl-3.0 2.8 M
Removing for dependencies:
ossec-hids-server x86_64 2.7-20.el6.art @asl-3.0 6.3 M

Transaction Summary
===========================================================================================================================================================================================================================================
Remove 2 Package(s)

Installed size: 9.1 M
Is this ok [y/N]:

This is in a vm so I can snapshot and try a few things, and revert if it all goes sideways ..

[breun]

Using your example, If you tagged mysql-libs-5.5.30 with Obsoletes: mysqlclient18 its going to do exactly what you told it to. Meaning mysqlclient18 will be upgraded over with mysql-libs-5.5.30. Which means that mysql-libs-5.1.67 would also be upgraded by mysql-libs-5.5.30 ( %{name} is identical on both packages). And since mysql-server-5.1.67 Requires: on mysql-libs-5.1.67, this too would be upgraded to mysql-server 5.5.30 since the mysql-libs-5.1.67 package is no longer installed. Ultimately this would disallow the condition of having a mysql 5.1 server, with both mysql 5.1 and 5.5 libraries.

When I want to have MySQL 5.1 on EL6 I exclude mysql-* from Atomic. I then still get mysqlclient18 for apps that need it for the 5.5 lib.

[Highland]

I cannot preach the virtues of php-mysqlnd enough. Just say no to mysqlclientXX!

[breun]

I cannot preach the virtues of php-mysqlnd enough. Just say no to mysqlclientXX!

Sadly that only works for PHP though.