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Issue Upgrading from MySql 5.5 to 5.6 on CentOS 6

D

Drewski

New Pleskian
I am following the guide here: How to upgrade MySQL 5.5 to 5.6/5.7 or MariaDB 5.5 to 10.0/10.1/10.2 on Linux

when I get to the step

# yum update mysql

I get this output:

Loaded plugins: fastestmirror
Setting up Update Process
Loading mirror speeds from cached hostfile
* base: mirrors.centos.webair.com
* epel: ewr.edge.kernel.org
* extras: mirror.ash.fastserv.com
* updates: mirrors.greenmountainaccess.net
Resolving Dependencies
--> Running transaction check
---> Package mysql.x86_64 0:5.5.30-1.el6.remi will be obsoleted
--> Processing Dependency: mysql(x86-64) = 5.5.30-1.el6.remi for package: mysql-bench-5.5.30-1.el6.remi.x86_64
--> Processing Dependency: mysql(x86-64) = 5.5.30-1.el6.remi for package: mysql-server-5.5.30-1.el6.remi.x86_64
--> Processing Dependency: mysql(x86-64) = 5.5.30-1.el6.remi for package: mysql-devel-5.5.30-1.el6.remi.x86_64
---> Package mysql-community-client.x86_64 0:5.6.41-2.el6 will be obsoleting
--> Processing Dependency: mysql-community-libs(x86-64) >= 5.6.10 for package: mysql-community-client-5.6.41-2.el6.x86_64
--> Running transaction check
---> Package mysql-bench.x86_64 0:5.5.30-1.el6.remi will be obsoleted
---> Package mysql-community-bench.x86_64 0:5.6.41-2.el6 will be obsoleting
---> Package mysql-community-devel.x86_64 0:5.6.41-2.el6 will be obsoleting
---> Package mysql-community-libs.x86_64 0:5.6.41-2.el6 will be obsoleting
--> Processing Dependency: mysql-community-common(x86-64) >= 5.6.10 for package: mysql-community-libs-5.6.41-2.el6.x86_64
---> Package mysql-community-server.x86_64 0:5.6.41-2.el6 will be obsoleting
--> Processing Dependency: libnuma.so.1(libnuma_1.2)(64bit) for package: mysql-community-server-5.6.41-2.el6.x86_64
--> Processing Dependency: libnuma.so.1(libnuma_1.1)(64bit) for package: mysql-community-server-5.6.41-2.el6.x86_64
--> Processing Dependency: libnuma.so.1()(64bit) for package: mysql-community-server-5.6.41-2.el6.x86_64
---> Package mysql-devel.x86_64 0:5.5.30-1.el6.remi will be obsoleted
---> Package mysql-libs.x86_64 0:5.5.30-1.el6.remi will be obsoleted
--> Processing Dependency: libmysqlclient.so.18(libmysqlclient_16)(64bit) for package: php-mysql-5.4.13-1.el6.remi.x86_64
---> Package mysql-server.x86_64 0:5.5.30-1.el6.remi will be obsoleted
--> Running transaction check
---> Package mysql-community-common.x86_64 0:5.6.41-2.el6 will be installed
---> Package mysql-libs.x86_64 0:5.5.30-1.el6.remi will be obsoleted
--> Processing Dependency: libmysqlclient.so.18(libmysqlclient_16)(64bit) for package: php-mysql-5.4.13-1.el6.remi.x86_64
---> Package numactl.x86_64 0:2.0.9-2.el6 will be installed
--> Finished Dependency Resolution
Error: Package: php-mysql-5.4.13-1.el6.remi.x86_64 (installed)
Requires: libmysqlclient.so.18(libmysqlclient_16)(64bit)
Removing: mysql-libs-5.5.30-1.el6.remi.x86_64 (installed)
libmysqlclient.so.18(libmysqlclient_16)(64bit)
Obsoleted By: mysql-community-libs-5.6.41-2.el6.x86_64 (mysql56-community)
Not found
Available: mysql-libs-5.5.28-3.el6.remi.x86_64 (mt_dv_extras)
libmysqlclient.so.18(libmysqlclient_16)(64bit)
Available: mysql-libs-5.5.29-1.el6.remi.x86_64 (mt_dv_extras)
libmysqlclient.so.18(libmysqlclient_16)(64bit)
Available: mysql-libs-5.1.73-8.el6_8.i686 (base)
Not found
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest


Any help is appreciated, thank you.
 
Drewski said:
Loading mirror speeds from cached hostfile
* base: mirrors.centos.webair.com
* epel: ewr.edge.kernel.org
* extras: mirror.ash.fastserv.com
* updates: mirrors.greenmountainaccess.net
Resolving Dependencies
--> Running transaction check
---> Package mysql.x86_64 0:5.5.30-1.el6.remi will be obsoleted
Click to expand...

You apparently have/had multiple sql versions installed. Your list of repos does not include remi, however you system still has an sql server of the remi repo installed. You must have had the remi repo enabled on your system at some point in the past.
Remove the remi sql package (just as you removed the atomic repo one) and you should be ready to carry on :)

Cheers,
Tom
 
Thanks for the reply Tom!

As you said, I don't appear have the remi repo enabled. yum repolist gives me:

repo id repo name status
PLESK_17_8_11-extras PLESK_17_8_11 extras 33
PLESK_17_PHP52 PHP 5.2 for Plesk 17 30
PLESK_17_PHP53 PHP 5.3 for Plesk 17 31
PLESK_17_PHP54 PHP 5.4 for Plesk 17 32
PLESK_17_PHP55 PHP 5.5 for Plesk 17 31
PLESK_17_PHP56 PHP 5.6 for Plesk 17 31
base CentOS-6 - Base 6,713
epel Extra Packages for Enterprise Linux 6 - x86_64 12,521
extras CentOS-6 - Extras 31
mt_dv_extras mediatemple extra packages for (dv) 1,104
mysql-connectors-community MySQL Connectors Community 59
mysql-tools-community MySQL Tools Community 65
mysql56-community MySQL 5.6 Community Server 453
plesk-migrator Plesk packages for migrator 9
plesk-migrator-tp Plesk 3d-party packages for migrator 0
updates CentOS-6 - Updates

However, when I run yum list installed | grep mysql I get this output:

compat-mysql51.x86_64 5.1.54-1.el6.remi installed
mysql.x86_64 5.5.30-1.el6.remi installed
mysql-bench.x86_64 5.5.30-1.el6.remi installed
mysql-connector-odbc.x86_64 5.1.5r1144-7.el6 installed
mysql-devel.x86_64 5.5.30-1.el6.remi installed
mysql-libs.x86_64 5.5.30-1.el6.remi installed
mysql-server.x86_64 5.5.30-1.el6.remi installed
mysql57-community-release.noarch
el6-7 @/mysql57-community-release-el6-7.noarch
php-mysql.x86_64 5.4.13-1.el6.remi installed
plesk-mysql-server.x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist
plesk-php52-mysql.x86_64 5.2.17-centos6.15100614 @PHP_5_2_17-dist
plesk-php53-mysql.x86_64 5.3.29-centos6.15102117 @PHP_5_3_29-dist
plesk-php54-mysql.x86_64 5.4.45-centos6.16032517 @PHP_5_4_45-dist
plesk-php55-mysql.x86_64 5.5.38-centos6.17031317 @PHP_5_5-dist
plesk-php56-mysql.x86_64 5.6.37-centos6.18072013 @PLESK_17_PHP56
 
So it looks like the only mysql I have is the remi one. I tried

yum remove mysql.x86_64 mysql-bench.x86_64 mysql-devel.x86_64 mysql-libs.x86_64 mysql-server.x86_64 php-mysql.x86_64

and got this output:
Removing:
mysql x86_64 5.5.30-1.el6.remi installed 28 M
mysql-bench x86_64 5.5.30-1.el6.remi installed 2.6 M
mysql-devel x86_64 5.5.30-1.el6.remi installed 598 k
mysql-libs x86_64 5.5.30-1.el6.remi installed 4.1 M
mysql-server x86_64 5.5.30-1.el6.remi installed 45 M
php-mysql x86_64 5.4.13-1.el6.remi installed 447 k
Removing for dependencies:
miva-ssl-stub i386 1.0.1-0.287001 installed 3.3 k
mt-custom-dv5 noarch 0.6.300018-1.el6 installed 30 k
plesk-base x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 17 k
plesk-billing noarch 12.0.18-20140520.11 installed 117 M
plesk-completion noarch 17.8.11-cos6.build1708180322.11 @PLESK_17_8_11-dist 2.1 M
plesk-core x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 101 M
plesk-dovecot x86_64 2.3.0.1-centos6.18031217 @PLESK_17_8_11-dist 3.7 M
plesk-dovecot-imap-driver x86_64 17.8.11-cos6.build1708180312.17 @PLESK_17_8_11-dist 388 k
plesk-dovecot-pigeonhole x86_64 0.5.0.1-centos6.18031217 @PLESK_17_8_11-dist 2.2 M
plesk-ext-catalog noarch 1.1.0-148.18030120 @PLESK_17_8_11-dist 1.0 M
plesk-ext-rest-api noarch 1.0.0-32.18030120 @PLESK_17_8_11-dist 2.1 M
plesk-l10n noarch 17.8.11-cos6.build1708180328.11 @PLESK_17_8_11-dist 58 M
plesk-mail-pc-driver x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 6.8 M
plesk-management-node x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 0.0
plesk-modsecurity-configurator noarch 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 46 k
plesk-mysql-server x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 0.0
plesk-roundcube noarch 1.3.6-cos6.build1708180427.13 @PLESK_17_8_11-dist 22 M
plesk-service-node-utilities x86_64 17.8.11-cos6.build1708180515.21 @PLESK_17_8_11-dist 13 M
plesk-web-hosting x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 173 k
plesk-wp-upgrade noarch 1.0-71.17061316 @PLESK_17_8_11-dist 11 M
pp-sitebuilder noarch 17.8.12-18032617 @SITEBUILDER_17_8_12-dist 0.0
pp12.0.18-bootstrapper x86_64 12.0.18-cos6.build1200151014.14 @PSA_12_0_18-dist 683 k
pp17.5.3-bootstrapper x86_64 17.5.3-cos6.build1705170317.16 @PLESK_17_5_3-dist 741 k
pp17.8.11-bootstrapper x86_64 17.8.11-cos6.build1708180515.14 @PLESK_17_8_11-dist 654 k
psa-drweb-configurator x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 441 k
psa-fileserver x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 1.1 M
psa-firewall x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 1.3 M
psa-horde noarch 5.2.17-cos6.build1708180425.15 @PLESK_17_8_11-dist 68 M
psa-imp noarch 6.2.21.1-cos6.build1708180425.15 @PLESK_17_8_11-dist 18 M
psa-ingo noarch 3.2.16-cos6.build1708180425.15 @PLESK_17_8_11-dist 4.5 M
 
psa-kronolith noarch 4.2.23-cos6.build1708180425.15 @PLESK_17_8_11-dist 9.0 M
psa-libpam-plesk x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 744 k
psa-libxml-proxy x86_64 2.9.7-centos6.18021314 @PLESK_17_8_11-dist 2.0 M
psa-locale-base-en-US noarch 17.8.11-cos6.build1708180823.15 @PLESK_17_8_11-dist 1.8 M
psa-logrotate x86_64 3.8.2-cos6.build1708171004.18 @PLESK_17_8_11-dist 101 k
psa-mail-driver-common x86_64 17.8.11-cos6.build1708180424.19 @PLESK_17_8_11-dist 2.6 M
psa-mailman-configurator x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 0.0
psa-miva x86_64 1:5.06-cos6.build1200140526.11 installed 4.5 M
psa-mnemo noarch 4.2.14-cos6.build1708180425.15 @PLESK_17_8_11-dist 3.3 M
psa-passwd noarch 5.0.7-cos6.build1708180425.15 @PLESK_17_8_11-dist 2.9 M
psa-php5-configurator x86_64 1.7.0-cos6.build1708180212.17 @PLESK_17_8_11-dist 56 k
psa-phpmyadmin noarch 4.7.8-cos6.build1708180222.17 @PLESK_17_8_11-dist 34 M
psa-proftpd x86_64 1.3.6-cos6.build1708180220.17 @PLESK_17_8_11-dist 7.9 M
psa-pylibplesk x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 90 k
psa-spamassassin x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 117 k
psa-turba noarch 4.2.21-cos6.build1708180425.15 @PLESK_17_8_11-dist 6.2 M
psa-updates noarch 17.8.11-cos6.build1708180326.12 @PLESK_17_8_11-dist 0.0
psa-vhost noarch 17.8.11-cos6.build1708180425.13 @PLESK_17_8_11-dist 299 k
psa-vpn x86_64 17.8.11-cos6.build1708180301.19 @PLESK_17_8_11-dist 2.9 M
wpb-core noarch 17.8.12-43703.18032617 @SITEBUILDER_17_8_12-dist 49 M
wpb-headers noarch 17.8.12-43703.18032617 @SITEBUILDER_17_8_12-dist 143 M

Transaction Summary
=================================================================================================================================================================================================================================
Remove 57 Package(s)

Obviously it seems I don't want to remove all those packages, so I am not sure how to continue.
 
Try removing the remi packages using the RPM command, nodeps as needed.

# rpm -e --nodeps blahblahblah
 
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