Skip to main content

Update server fail .. need assistance

Bill Fleming

I am not sure why it trying to install mysql update and failed when I am only using Maria on WHM / cPanel 

Any idea why the server is trying to update mysql and failing the update when it conflict with Maria.   mysql isn't installed on this server 





Error: Transaction test error:
  file /usr/share/mysql/charsets/Index.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/armscii8.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/ascii.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp1250.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp1251.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp1256.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp1257.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp850.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp852.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp866.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/dec8.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/geostd8.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/greek.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/hebrew.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/hp8.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/keybcs2.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/koi8r.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/koi8u.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/latin1.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/latin2.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/latin5.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/latin7.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/macce.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/macroman.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/swe7.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64

(XID fyuzkb) “/usr/bin/yum” reported error code “1” when it ended:

Comments

18 comments

Date Votes
  • cPRex Jurassic Moderator

    Can you share the output of the following two commands?

    rpm -qa | grep -i mysql
    rpm -qa | grep -i maria

    and that should give us some more details.

    0
  • Bill Fleming

    [root@ns5 ~]# rpm -qa | grep -i mysql
    rpm -qa | grep -i maria
    perl-DBD-MySQL-4.050-13.el9.x86_64
    mysql-selinux-1.0.14-1.el9_6.noarch
    ea-php81-php-mysqlnd-8.1.33-3.6.1.cpanel.x86_64
    ea-php82-php-mysqlnd-8.2.29-3.6.1.cpanel.x86_64
    ea-php80-php-mysqlnd-8.0.30-9.15.1.cpanel.x86_64
    ea-php83-php-mysqlnd-8.3.27-2.5.1.cpanel.x86_64
    cpanel-perl-542-mysql-diff-0.60-1.cp130~el9.noarch
    cpanel-perl-542-dbd-mysql-4.050-1.cp130~el9.x86_64
    MariaDB-shared-10.11.15-1.el9.x86_64
    MariaDB-common-10.11.15-1.el9.x86_64
    MariaDB-client-10.11.15-1.el9.x86_64
    MariaDB-server-10.11.15-1.el9.x86_64
    MariaDB-devel-10.11.15-1.el9.x86_64
    cpanel-mariadb-connector-3.3.15-2.cp130~el9.x86_64
    cpanel-mariadb-connector-devel-3.3.15-2.cp130~el9.x86_64
    [root@ns5 ~]#

    0
  • cPRex Jurassic Moderator

    I can't tell from the output if that was run as two separate commands so I can't tell for sure, but there definitely seems to be some conflict on the database version installed on the machine.

    Let's try this command instead:

    rpm -qf /usr/share/mysql/charsets/cp866.xml

    Can you paste the output of that here?  That should tell us what package it thinks owns that file.

    0
  • Bill Fleming

    [root@ns5 ~]# rpm -qf /usr/share/mysql/charsets/cp866.xml
    MariaDB-common-10.11.15-1.el9.x86_64
    [root@ns5 ~]#

    0
  • cPRex Jurassic Moderator

    Alright, so that's good.

    One last thing before I recommend some action:

    ls -lah /etc/yum.repos.d | grep -i mysql
    0
  • Bill Fleming

    I ran the command you requested:

    ls -lah /etc/yum.repos.d | grep -i mysql

    There was no output, so there are no MySQL repo files present on this server.

    Based on the previous testing, it looks like the mysql-common-8.0.43 package is coming from the AlmaLinux AppStream repo. The MariaDB1011 repo already provides the correct MariaDB-common package, so AppStream is trying to offer mysql-common, which conflicts with MariaDB-common during updates.

    Let me know what the next recommended step is. I’m happy to run any additional commands you need.

    0
  • cPRex Jurassic Moderator

    Interesting - let's try this and see if that works:

    mv /usr/share/mysql/ /usr/share/mysql.bak

    so that directory can't be read by the system.  Can you do that and then try the update and see if that works better?

    0
  • Bill Fleming

    Same thing 

    Transaction check succeeded.
Running transaction test
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'yum clean packages'.
Error: Transaction test error:
  file /usr/share/mysql/charsets/Index.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/armscii8.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/ascii.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp1250.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp1251.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp1256.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp1257.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp850.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp852.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/cp866.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/dec8.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/geostd8.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/greek.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/hebrew.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/hp8.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/keybcs2.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/koi8r.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/koi8u.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/latin1.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/latin2.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/latin5.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/latin7.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/macce.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/macroman.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
  file /usr/share/mysql/charsets/swe7.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64

(XID eqt8mw) “/usr/bin/yum” reported error code “1” when it ended:
    0
  • Bill Fleming

    I added the mysql* MySQL* patterns to the exclude line in both yum and dnf:

    exclude=bind-chroot dovecot* exim* filesystem p0f php* proftpd* pure-ftpd* mysql* MySQL*

    However, the system is still trying to install mysql-common during the update, and I continue to get the same file conflicts with MariaDB-common.

    Error example:
    file /usr/share/mysql/charsets/Index.xml from install of mysql-common-8.0.43-1.el9_6.x86_64 conflicts with file from package MariaDB-common-10.11.15-1.el9.x86_64
    (and multiple similar charset file conflicts)

    There are no MySQL repo files in /etc/yum.repos.d, so the mysql-common package is coming from the AlmaLinux AppStream repo. It looks like something is still pulling mysql-common into the transaction even with the exclude rules applied.

    This issue may have started right after the last AlmaLinux OS update, since everything was working normally before then.

    Let me know what the next recommended step is or how to prevent AppStream from trying to install mysql-common alongside MariaDB.

    0
  • cPRex Jurassic Moderator

    cPanel has certain things where it will override the exclude - this may be one of those cases as the database is a system-critical component.

    Your output, at least the way I'm reading it, doesn't show that it's trying to install anything from MySQL, but that leftover files on the server are conflicting with new files from the MariaDB update.  That's why i recommended just trying to move that directory aside and seeing what happens.

    0
  • Bill Fleming

    I did move that directory aside and it still giving the conflict error. 

    0
  • cPRex Jurassic Moderator

    At this point I'm not sure then - it would be best to create a ticket so this can be examined directly.  I'd hate to recommend something that could take a service offline.

    0
  • Bill Fleming

    I tried to open a support ticket, but the system told me that ticket support is only available to customers who purchased their cPanel license directly from cPanel. I do have an active cPanel license, but it is provided through cPanel subscription service rather than purchased directly.

    Is there any way for someone in my situation to receive support? If direct ticket access is not available, what is the correct process to get assistance? 

    0
  • cPRex Jurassic Moderator

    You would open the ticket with your license provider and they should be able to handle anything for you: https://support.cpanel.net/hc/en-us/community/posts/35919412082327-Confusion-around-Partner-Support-licenses-and-contacting-cPanel-support

    0
  • Dexter Ang

    The mysql-common and mysql-libs is a dependency of the latest perl-DBD-MySQL 4.053-1.el9 update it seems. Previous version (4.050-13.el9) doesn't seem to need them.

    0
  • cPRex Jurassic Moderator
    • Edited

    Our team has reported this behavior to MySQL as part of case CPANEL-50477, so both us and MySQL are working on this now.  In the mean time, the ultimate resolution is to manually uninstall the old version for MySQL, and manually install the new version for MariaDB before any updates happen:

    dnf remove perl-DBD-MySQL
    dnf install perl-DBD-MariaDB

    and after doing that you should be able to update the system normally.

    0
  • Bill Fleming

    The update completed normally after I applied your fix. 

    Thank you
    Bill

    0
  • cPRex Jurassic Moderator

    I'm so glad to hear it, and glad that we finally got to a resolution!

    0

Please sign in to leave a comment.

Didn't find what you were looking for?

New post