Upgraded MySQL with the cPanel interface and now cPanel is sending warnings about MySQL RPMs

[iaresee]

I used the CPanel WHM interface to move MySQL from v5.0 to 5.6 earlier this week. Last night I got an email from my system that claims there are now problems with older MySQL RPMs. The email said:

Problems were detected with cPanel-provided files which are RPM controlled.
If you did not make these changes intentionally, you can correct them by running:

> /usr/local/cpanel/scripts/check_cpanel_rpms --fix

The following RPMs are found to be altered from their original install state: 
compat-MySQL51-shared,5.1.73,4.cp1136,/usr/lib64/libmysqlclient.so.16.0.0

And when I ran check_cpanel_rpms on the machine I got:

> /usr/local/cpanel/scripts/check_cpanel_rpms --list-only
prelink: /usr/lib64/libmysqlclient.so.16.0.0: at least one of file's dependencies has changed since prelinking
[20141025.184811]
[20141025.184811]   Problems were detected with cPanel-provided files which are RPM controlled.
[20141025.184811]   If you did not make these changes intentionally, you can correct them by running:
[20141025.184811]
[20141025.184811]   > /usr/local/cpanel/scripts/check_cpanel_rpms --fix
[20141025.184811]
[20141025.184811]   The following files were found to be altered from their original RPM:
[20141025.184811]   compat-MySQL51-shared,5.1.73,4.cp1136
[20141025.184811]

Seems a little odd it's complaining about 5.1 RPMs given the system is at 5.6 now. I'd like to get rid of the warning. I noticed another post where the solution seemed to be "run the entire 5.6 upgrade again". That seems like a VERY big hammer to swing to fix a warning about RPMs that aren't even in use on the system.

Running the script with the --fix option has a "magic" outcome -- what exactly happens when you use that option? Given that it's complaining about a binary I'm worried it'll change components needed by the running MySQL instance.

Is there a gentler way to correct this warning? Preferably one that doesn't involve a MySQL outage?

 

[iaresee]

To follow up, I posted this on SuperUser as well /http://superuser.com/questions/832077/cpanel-is-warning-about-inconsistent-rpms-for-an-old-mysql-installation-how-d and got some reassurance that --fix wouldn't take down my running MySQL installation.

I went ahead and ran it. It did down and install the compat-MySQL51-shared-5.1.73-4.cp1136.x86_64.rpm RPM but my 5.6 server and command line remained untouched and running. My PHP extensions all still link against the 5.6 version.

Output was:

# /usr/local/cpanel/scripts/check_cpanel_rpms --fix
prelink: /usr/lib64/libmysqlclient.so.16.0.0: at least one of file's dependencies has changed since prelinking
[20141027.000109]
[20141027.000109]   Problems were detected with cPanel-provided files which are RPM controlled.
[20141027.000109]   If you did not make these changes intentionally, you can correct them by running:
[20141027.000109]
[20141027.000109]   > /usr/local/cpanel/scripts/check_cpanel_rpms --fix
[20141027.000109]
[20141027.000109]   The following files were found to be altered from their original RPM:
[20141027.000109]   compat-MySQL51-shared,5.1.73,4.cp1136
[20141027.000109]
[20141027.000109]   Removing 1 broken rpms: compat-MySQL51-shared-5.1.73-4.cp1136.x86_64
[20141027.000110]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/6/x86_64/rpm.md5
[20141027.000110]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/6/x86_64/compat-MySQL51-shared-5.1.73-4.cp1136.x86_64.rpm
[20141027.000111]   Hooks system enabled
[20141027.000111]   Checking for and running RPM::Versions 'pre' hooks for any RPMs about to be installed
[20141027.000111]   All required 'pre' hooks have been run
[20141027.000111]   No RPMS need to be uninstalled
[20141027.000111]   Installing new rpms: compat-MySQL51-shared-5.1.73-4.cp1136.x86_64.rpm
[20141027.000111]   Preparing packages for installation...
[20141027.000111]   compat-MySQL51-shared-5.1.73-4.cp1136
[20141027.000111]   Prelinking shared libraries and binaries: /usr/sbin/prelink -av -mR
[20141027.000116]   Checking for and running RPM::Versions 'post' hooks for any RPMs just installed
[20141027.000116]   All required 'post' hooks have been run

So, problem solved.

 

[cPanelMichael]

Hello

I am happy to see you were able to resolve the issue. Thank you for updating us with the outcome.

 

[tss]

Hello

I am happy to see you were able to resolve the issue. Thank you for updating us with the outcome.

Please provide an explanation, which no one in any of these posts has provided. How does this make sense? I used WHM to upgrade MySQL from 5.0 to 5.5 and am getting the same warning. The warning says "If you did not make these changes intentionally", but of course, upgrading cPanel WAS done intentionally. So how was this RPM "changed"? And changed from what? And if compat-MySQL51-shared-5.1.73-4.cp1136.x86_64.rpm is necessary for running MySQL 5.5 or 5.6, why are our servers in fact working? This is obviously NOT a MySQL-provided file, but a cPanel provided one. Why didn't cPanel install this RPM during the upgrade? And why does anything in cPanel have to be compatible with MySQL 5.1? What functionality is being lost by NOT installing this RPM?

While I'm getting tired of the nightly emails, I also don't see the point in installing an unnecessary RPM just to get cPanel to stop its (seemingly erroneous) complaining.

Seems like a bug in cPanel to me. Please tell us why if it's not.

 

[cPanelMichael]

Hello

The post before mine suggests that running the following command resolved their issue:

/usr/local/cpanel/scripts/check_cpanel_rpms --fix

The "compat-MySQL51-shared,5.1.73,4.cp1136" RPM is required per internal case number 104745. This provides a method for users to upgrade MySQL without rebuilding PHP.

Thank you.