Question Upgrade to MYSQL 5.6 says 5.1 is still present and can't upgrade

[Willem Janssen]

Almost a year ago I upgraded Mysql 5.1 to 5.5 through Atomic. Not the best choice .

OS: ‪CentOS 6.8 (Final)‬
Product: Plesk Onyx 17.0.17 Update #18 , last updated at Mar 6, 2017 09:58 AM

When I run mysqld -V it shows:
mysqld Ver 5.5.54 for Linux on x86_64 (MySQL Community Server (GPL))

That's obviously great but when I run 'yum install mysql' (I followed the howto: https://support.plesk.com/hc/en-us/articles/213403429-How-to-upgrade-MySQL-5-5-to-5-6) it says:
Package mysql-5.1.73-8.el6_8.x86_64 is obsoleted by mysql-community-client-5.5.54-2.el6.x86_64 which is already installed

Did a 'package-cleanup --orphans' check.
When trying to remove mysql 5.1 it shows it still has a lot of dependencies (see below). Is it safe to remove them?

Dependencies Resolved

===================================================================================================================================================
Package Arch Version Repository Size
===================================================================================================================================================
Removing:
mysqlclient16 x86_64 5.1.59-2.el6.art @atomic 4.1 M
Removing for dependencies:
cloudflare-servershield x86_64 1.8-1.centos6.15081910 @PSA_12_0_18-dist 448 k
cronie x86_64 1.4.4-16.el6_8.2 @updates 174 k
cronie-anacron x86_64 1.4.4-16.el6_8.2 @updates 43 k
crontabs noarch 1.10-33.el6 @anaconda-CentOS-201303020151.x86_64/6.4 2.4 k
perl-DBD-MySQL x86_64 4.013-3.el6 @base 338 k
php-mysql x86_64 5.4.45-56.el6.art @atomic 1.8 M
plesk-config-troubleshooter x86_64 17.0.17-cos6.build1700161028.14 @PLESK_17_0_17-dist 391 k
plesk-core x86_64 17.0.17-cos6.build1700161028.14 @PLESK_17_0_17-dist 48 M
plesk-l10n noarch 17.0.17-cos6.build1700170119.11 @PLESK_17_0_17-dist 58 M
plesk-mail-pc-driver x86_64 17.0.17-cos6.build1700161215.15 @PLESK_17_0_17-dist 6.4 M
plesk-management-node x86_64 17.0.17-cos6.build1700161028.14 @PLESK_17_0_17-dist 0.0
postfix x86_64 2:2.11.5-centos6.16102516 installed 14 M
psa-drweb-configurator x86_64 17.0.17-cos6.build1700161028.14 @PLESK_17_0_17-dist 444 k
psa-firewall x86_64 17.0.17-cos6.build1700161028.14 @PLESK_17_0_17-dist 649 k
psa-php5-configurator x86_64 1.7.0-cos6.build1700161026.16 @PLESK_17_0_17-dist 55 k
psa-spamassassin x86_64 17.0.17-cos6.build1700161028.14 @PLESK_17_0_17-dist 103 k
psa-updates noarch 17.0.17-cos6.build1700161025.15 @PLESK_17_0_17-dist 0.0
psa-watchdog x86_64 17.0.17-cos6.build1700161028.14 @PLESK_17_0_17-dist 3.0 M

Transaction Summary
===================================================================================================================================================
Remove 19 Package(s)

 

[UFHH01]

Hi Willem Janssen,

actually, you should be informed about the fact, that when you DISABLE a specific repo, you might get some misleading informations about dependencies. You probably disabled the atomic - repo ( as suggested in the KB - article ) and experience now, that a check points out essential, needed packages, which you definetly don't want to remove on your server.

As you already noticed as well, you previous mysql - upgrade wasn't really a good choice. You still could remove "mysql-5.1.73-8.el6_8.x86_64" with "rpm", but with the option to ignore dependencies.

Example:

rpm -qa | grep "mysql-5.1"
mysql-5.1.73-8.el6_8.x86_64
rpm -e --nodeps "mysql-5.1.73-8.el6_8.x86_64"

Afterwards, pls. go back to the step "yum install mysql" and continue as suggested in the KB - article. If you experience errors/issues/problems, while removing a package with the "--nodeps" - flag, pls. report back, so people willing to help you might suggest possible additional commands.

 

[Willem Janssen]

Hi UFHH01,

Thanks for your tip !

rpm -qa | grep "mysql-5.1" -- doesn't do anything
rpm -e --nodeps "mysql-5.1.73-8.el6_8.x86_64" -- error: package mysql-5.1.73-8.el6_8.x86_64 is not installed
yum install mysql still shows me the same error "Package mysql-5.1.73-8.el6_8.x86_64 is obsoleted by mysql-community-client-5.5.54-2.el6.x86_64 which is already installed
Nothing to do"

Weird error

 

[UFHH01]

rpm -qa | grep "mysql-5.1" -- doesn't do anything

Pls. use then

rpm -qa | grep "mysql" and pls. DON'T continue with further suggestions as for example "rpm -e --nodeps ...", because it's pretty useless to try to remove a package, which you didn't find with the package - manager. ^^

The command "rpm -qa" lists the INSTALLED packages on your server, while the "grep" - command can be used, to reduce the output to the choosen option ( name ).

 

[Willem Janssen]

rpm -qa | grep "mysql" result:
plesk-php71-mysql-7.1.2-centos6.17021713.x86_64
mysql-community-client-5.5.54-2.el6.x86_64
php-mysql-5.4.45-56.el6.art.x86_64
mysql57-community-release-el6-7.noarch
mysql-connector-odbc-5.3.7-1.el6.x86_64
mysql-community-libs-5.5.54-2.el6.x86_64
mysql-community-server-5.5.54-2.el6.x86_64
plesk-mysql-server-17.0.17-cos6.build1700161028.14.x86_64
mysql-community-common-5.5.54-2.el6.x86_64

Mysql 5.1 isn't there but still shows the error 'Package mysql-5.1.73-8.el6_8.x86_64 is obsoleted by mysql-community-client-5.5.54-2.el6.x86_64 which is already installed
Nothing to do'.

When I perform 'yum update mysql' it installs the new version but when I want to upgrade the databases it fails;
MYSQL_PWD=`cat /etc/psa/.psa.shadow` mysql_upgrade -uadmin psa
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
Error: Failed while fetching Server version! Could be due to unauthorized access.
FATAL ERROR: Upgrade failed

 

[UFHH01]

Hi Willem Janssen,

sorry, but "guessing" will not really point to issues/errors/problems, I'm afraid, but FACTS may do this.

If you think, that a package might be a root cause of an issue, consider to check its dependencies:

yum deplist php-mysql​

 

[Willem Janssen]

Hi UFHH01,

There's unfortunately no guessing when dealing with facts

Tried to upgrade mysql (it completed without any fails) but when upgrading the DB it failed:
MYSQL_PWD=`cat /etc/psa/.psa.shadow` mysql_upgrade -uadmin psa
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
Error: Failed while fetching Server version! Could be due to unauthorized access.
FATAL ERROR: Upgrade failed

 

[UFHH01]

Hi Willem Janssen,

somewhere in your previous steps, there has been a mistake, which could now result in a mismatch of your password. Try to check that with for example:

cat /etc/psa/.psa.shadow
mysql -uadmin -pYOUR-CURRENT-ENCRYPTED-PASSWORD-FROM-psa.shadow

"exit", if you are able to login and check as well if the following command will as well succeed to login into MySQL, using the DB "psa".

plesk db​