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I am running Centos 5.8 (Linux 2.6.18-308.13.1.el5 on x86_64), and wish to upgrade MySQL version 5.0.95. I am using a tutorial found at http://www.if-not-true-then-false.com/2010/install-mysql-on-fedora-centos-red-hat-rhel/. When I get to the following, I get the host of errors. Seems to have something to do with going from 386 to 86x64. Can anyone help? Thanks

yum --enablerepo=remi,remi-test update mysql mysql-server

Transaction Check Error:   file /etc/my.cnf from install of
mysql50-5.0.96-2.ius.el5.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/info/mysql.info.gz from
install of mysql50-5.0.96-2.ius.el5.x86_64 conflicts with file from
package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/man/man1/mysql.1.gz from install of
mysql50-5.0.96-2.ius.el5.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/man/man1/mysqlaccess.1.gz from install of
mysql50-5.0.96-2.ius.el5.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/man/man1/mysqladmin.1.gz
from install of mysql50-5.0.96-2.ius.el5.x86_64 conflicts with file
from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/man/man1/mysqldump.1.gz from install of
mysql50-5.0.96-2.ius.el5.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/man/man1/mysqlshow.1.gz
from install of mysql50-5.0.96-2.ius.el5.x86_64 conflicts with file
from package mysql-5.0.95-1.el5_7.1.i386   file /etc/my.cnf from
install of mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file
from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/charsets/Index.xml from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/charsets/cp1250.xml from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/charsets/cp1251.xml from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/mysql/czech/errmsg.sys
from install of mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with
file from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/danish/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/mysql/dutch/errmsg.sys
from install of mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with
file from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/english/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/estonian/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/mysql/french/errmsg.sys
from install of mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with
file from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/german/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/mysql/greek/errmsg.sys
from install of mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with
file from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/hungarian/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/mysql/italian/errmsg.sys
from install of mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with
file from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/japanese/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/mysql/korean/errmsg.sys
from install of mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with
file from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/norwegian-ny/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/norwegian/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/mysql/polish/errmsg.sys
from install of mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with
file from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/portuguese/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/romanian/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/mysql/russian/errmsg.sys
from install of mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with
file from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/serbian/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/mysql/slovak/errmsg.sys
from install of mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with
file from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/spanish/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/mysql/swedish/errmsg.sys
from install of mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with
file from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/mysql/ukrainian/errmsg.sys from install of
mysql-libs-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/bin/mysqlaccess from install
of mysql-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/man/man1/my_print_defaults.1.gz from install of
mysql-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/man/man1/mysql.1.gz from
install of mysql-5.5.28-1.el5.remi.x86_64 conflicts with file from
package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/man/man1/mysql_config.1.gz from install of
mysql-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/man/man1/mysql_find_rows.1.gz from install of
mysql-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/man/man1/mysql_waitpid.1.gz from install of
mysql-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/man/man1/mysqlaccess.1.gz from install of
mysql-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/man/man1/mysqladmin.1.gz
from install of mysql-5.5.28-1.el5.remi.x86_64 conflicts with file
from package mysql-5.0.95-1.el5_7.1.i386   file
/usr/share/man/man1/mysqldump.1.gz from install of
mysql-5.5.28-1.el5.remi.x86_64 conflicts with file from package
mysql-5.0.95-1.el5_7.1.i386   file /usr/share/man/man1/mysqlshow.1.gz
from install of mysql-5.5.28-1.el5.remi.x86_64 conflicts with file
from package mysql-5.0.95-1.el5_7.1.i386
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2 Answers

It appears from that output that it's trying to install the new version of mysql alongside the old version, rather than actually upgrading. This is likely explained by the fact that you are trying to install the x86_64 version, but previously you had the i386 version (I think that should be considered either a bug in yum or a bug in the repository you are using, and in fact here is the bug report).

Try explicitly specifying the i386 version of mysql, or using mysqldump to dump the entire instance, uninstalling, and then installing the x86_64 version and importing the dump (you can import dumps taken by mysqldump by piping them into mysql -p, as they are SQL scripts).

To update specifically the i386 version, change mysql mysql-server in your command to mysql.i386 mysql-server.i386.

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First tried the 386 solution. Received the following error. No Match for argument: mysql-server.i386 No package mysql-server.i386 available. No Packages marked for Update –  user1032531 Oct 21 '12 at 16:08
    
In that case there may not be one in the repository, in which case you will have to either find a repository that has one, or migrate to x64. –  Falcon Momot Oct 21 '12 at 16:14
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It looks like you've used MySQL packages from the IUS community repo. Unfortunately these packages don't appear to be 100% compatible with the original packages, and so you get broken dependencies such as this one. Remove all of the existing MySQL packages first (your databases won't be touched) and then install the packages from the remi repository (which ARE compatible and have no dependency issues).

You also need to be sure you have disabled or removed the conflicting repo (IUS).

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To remove, I tried yum remove mysql-server. Seems like I didn't remove all as I am still getting similar errors. –  user1032531 Oct 21 '12 at 17:05
    
rpm -aq | grep mysql | xargs rpm -e --nodeps --allmatches –  user1032531 Oct 21 '12 at 17:12
    
See edited answer. –  Michael Hampton Oct 21 '12 at 17:14
    
I don't see any dependencies at all in there, actually. It appears to be entirely a conflict; if I recall, yum (and apt) assumes that you can have x86 and x64 packages installed side by side. However, yes, using packages from different repositories that provide the same software is totally a bad idea. –  Falcon Momot Oct 21 '12 at 17:17
    
@FalconMomot Oh, it's worse. In this case, the 32-bit version mismatches the incompatible 64-bit version from the IUS repo. This should straighten itself out when he removes the IUS repo, as the existing packages could then be updated to match. (Though there's no reason to keep the 32-bit ones at all anyway...) –  Michael Hampton Oct 21 '12 at 22:45
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