Need serious help on Fedora (lost plesk)

[sector29]

Please excuse my ignorance but i think I uninstalled a lot of things I shouldn't have. This is not a slam of ART.

I was attempting to update mysql using ART's RPM and I lost Plesk and mysql.

I ran the RPMs using yum update and restarted mysql but noticed that mysql 3 was still running.

I found another post that suggested uninstalling mysql and installing the rpms so i did a yum remove mysql and a yum install mysql.

this is what caused me the problem because it appeared through ssh that a lot more than mysql was uninstalled. I saw a lot of plesk references fly by.

anyway, i can no longer access plesk at the 8443 port and i am unable to restart mysqld

my yum.conf looks like this:

[main]
cachedir=/var/cache/yum
debuglevel=2
logfile=/var/log/yum.log
pkgpolicy=newest
distroverpkg=redhat-release
tolerant=1
exactarch=1
retries=20

[base]
name=Fedora Core $releasever - $basearch - Base
baseurl=http://update.onlinehome-server.com/fedora/linux/core/$releasever/$basearch/os/

[atomic]
name=Atomic Rocket Turtle - $releasever - Atomic PSA-Compatible RPMS
baseurl=http://3es.atomicrocketturtle.com/atomic/art/$releasever/
baseurl=http://www.atomicrocketturtle.com/atomic/art/$releasever/

[updates-released]
name=Fedora Core $releasever - $basearch - Released Updates
baseurl=http://update.onlinehome-server.com/fedora/linux/core/updates/$releasever/$basearch/

#[updates-testing]
#name=Fedora Core $releasever - $basearch - Unreleased Updates
#baseurl=http://download.fedora.redhat.com/pub/fedora/linux/core/updates/testing/$releasever/$basearch/

#[development]
#name=Fedora Core $releasever - Development Tree
#baseurl=http://download.fedora.redhat.com/pub/fedora/linux/core/development/$basearch/

 

[jamesyeeoc]

I saw a lot of plesk references fly by.

I don't suppose you kept a copy of the SSH log or copy of the screen output to refer to?

These references should indicate which packages will need to be reinstalled.

You can also try manually re-installing Plesk by running the installer file from the SSH shell prompt. But it would be better to refer to the log/output to see exactly what was changed during the yum operation.

 

[sector29]

Hi James,

This is the SSH Log . Even though I can see what happened, I don't have a clue how to reverse it. It's a 1and1 server, so if I do have to fully reinstall all of this, please point me in the right direction. I won't receive help from 1and1, per 1and1 policy.
.
I'll have to split the post. Sorry if this is considered spamming.
.
.
<post 1>
[root@<domain>]# yum remove mysql
Gathering header information file(s) from server(s)
Server: Atomic Rocket Turtle - 2 - Atomic PSA-Compatible RPMS
Server: Fedora Core 2 - i386 - Base
Server: Fedora Core 2 - i386 - Released Updates
error: rpmdb: damaged header #53 retrieved -- skipping.
error: rpmdb: damaged header #241 retrieved -- skipping.
error: rpmdb: damaged header #253 retrieved -- skipping.
Finding updated packages
Downloading needed headers
Resolving dependencies
.....Dependencies resolved
I will do the following:
[erase: mysql 4.0.25-1.rhfc2.art.i386]
I will erase these to satisfy the dependencies:
[deps: psa-agent 1.3.5-75050824.12.noarch]
[deps: DocFAQ 1.71-7508.noarch]
[deps: php-mysql 4.3.10-2.4.i386]
[deps: psa-turba 2.0.3-fc2.build75050824.12.noarch]
[deps: AutoIndex 1.5.3-7507.noarch]
[deps: osCommerce 2.2ms2-7509.noarch]
[deps: psa-fileserver 1.0.0-fc2.build75050824.12.i586]
[deps: CSLH 2.12.2-7504.noarch]
[deps: psa-bu 7.5.4-fc2.build75050824.12.i586]
[deps: xrms 1.19-7504.noarch]
[deps: bbclone 0.48-7508.noarch]
[deps: phpAds 2.0.5-7506.noarch]
[deps: psa-api-rpc 7.5.4-fc2.build75050824.12.noarch]
[deps: phpMoney 1.3-7510.noarch]
[deps: phpWiki 1.3.11-7508.noarch]
[deps: phpsurveyor 0.98-7510.noarch]
[deps: psa-migration-manager 7.5.4-fc2.build75050824.12.i586]
[deps: sitebuilder_de_DE 1.0-0.i386]
[deps: psa-passwd 3.0-fc2.build75050824.12.noarch]
[deps: perl-DBD-MySQL 2.9003-4.i386]
[deps: phpBugTracker 1.19-7506.noarch]
[deps: psa-api-common 7.5.4-fc2.build75050824.12.noarch]
[deps: psa-kronolith 2.0.3-fc2.build75050824.12.noarch]
[deps: psa-mnemo 2.0.1-fc2.build75050824.12.noarch]
[deps: Mambo 4.5.2-7505.noarch]
[deps: SSHTerm 0.2.2-fc2.build75050824.12.noarch]
[deps: PostNuke 0.750-7505.noarch]
[deps: psa-manual-custom-skin-guide 7.5.4-fc2.build75050824.12.noarch]
[deps: psa-firewall 1.0.1-fc2.build75050824.12.i586]
[deps: Sitebuilder 1.1.1-fc2.build050629.12.i386]
[deps: frontpage 5.0-72psa.fc2.i586]
[deps: phpBook 1.50-7507.noarch]
[deps: phpBB 2.0.17-7505.noarch]
[deps: psa-ingo 1.0.1-fc2.build75050824.12.noarch]
[deps: psa-horde 3.0.5-fc2.build75050824.12.noarch]
[deps: mysql-server 4.0.25-1.rhfc2.art.i386]
[deps: pLog 1.0-7508.noarch]
[deps: TUTOS 1.88-7504.noarch]
[deps: Tellme 1.2-7507.noarch]
[deps: typo 3.8.0-7505.noarch]
[deps: Coppermine 1.3.3-7515.noarch]
[deps: psa-spamassassin 7.5.4-fc2.build75050824.12.i586]
[deps: mod_webapp 4.1.29-41psa.fc2.i586]
[deps: phpDig 1.85-7505.noarch]
[deps: PPWSE 1.1-fc2.build75050824.12.i586]
[deps: cs-gs 1.2.2-fc2.build75050824.12.i586]
[deps: WebCalendar 1.0-7504.noarch]
[deps: psa-api-cli 7.5.4-fc2.build75050824.12.noarch]
[deps: mysql-compat 4.0.25-1.rhfc2.art.i386]
[deps: WebShopmanager 2.0-7506.noarch]
[deps: UebiMiau 2.7.8-7508.noarch]
[deps: psa-vpn 1.0.0-fc2.build75050824.12.i586]
[deps: psa-bf1942 1.0.0-fc2.build75050824.12.i586]
[deps: psa-qmail-rblsmtpd 0.70-fc2.build75050824.12.i586]
[deps: psa-tomcat-configurator 7.5.4-fc2.build75050824.12.noarch]
[deps: openbiblio 0.5-7513.noarch]
[deps: phpMyFamily 1.4.1-7508.noarch]
[deps: psa 7.5.4-fc2.build75050824.12.i586]
[deps: b2evolution 0.9.0.12-7505.noarch]
[deps: gallery 2.0-7516.noarch]
[deps: gtchat 0.93-7507.noarch]
[deps: Owl 0.80-7507.noarch]
[deps: WordPress 1.5.1-7509.noarch]
[deps: AdvancedPoll 2.03-7505.noarch]
[deps: psa-imp 4.0.3-fc2.build75050824.12.noarch]
[deps: psa-sbm 1.1-35.noarch]
[deps: psa-watchdog 1.0.0-fc2.build75050824.12.i586]
Is this ok [y/N]: y
Downloading Packages
Running test transaction:
Test transaction complete, Success!
Erasing: psa-ingo 1/68
Erasing: DocFAQ 2/68
Erasing: php-mysql 3/68
Erasing: psa-turba 4/68
Erasing: AutoIndex 5/68
Erasing: osCommerce 6/68
===> Updating /etc/psa/psa.conf...
===> Unregistering module
===> Uninstalling configuration files
===> Uninstalling database
Erasing: psa-fileserver 7/68
Erasing: CSLH 8/68
Erasing: psa-bu 9/68
Erasing: xrms 10/68
Erasing: bbclone 11/68
Erasing: phpAds 12/68
===> Updating /etc/psa/psa.conf...
Erasing: psa-api-rpc 13/68
Erasing: phpMoney 14/68
Erasing: phpWiki 15/68
Erasing: phpsurveyor 16/68
Erasing: psa-migration-manager 17/68
Erasing: sitebuilder_de_DE 18/68
Erasing: psa-passwd 19/68
Erasing: perl-DBD-MySQL 20/68
Erasing: phpBugTracker 21/68
Erasing: psa-api-common 22/68
warning: /etc/my.cnf saved as /etc/my.cnf.rpmsave
Erasing: mysql 23/68
Erasing: psa-kronolith 24/68
Erasing: psa-mnemo 25/68
Erasing: Mambo 26/68
Erasing: SSHTerm 27/68
Erasing: PostNuke 28/68
Erasing: psa-manual-custom-skin-guide 29/68
===> Updating /etc/psa/psa.conf...
===> Unregistering module
/var/tmp/rpm-tmp.8498: line 2070: /usr/bin/mysql: No such file or directory
===> Uninstalling configuration files
Trying to unregister service psa-firewall... using /sbin/chkconfig
===> Uninstalling database
/var/tmp/rpm-tmp.8498: line 2049: /usr/bin/mysql: No such file or directory
/var/tmp/rpm-tmp.8498: line 2050: /usr/bin/mysql: No such file or directory
Erasing: psa-firewall 30/68
Erasing: Sitebuilder 31/68
=> Uninstalling Sitebuilder
Erasing: frontpage 32/68
Erasing: phpBook 33/68
Erasing: phpBB 34/68
Erasing: psa-horde 35/68
Erasing: mysql-server 36/68
Erasing: pLog 37/68
Erasing: TUTOS 38/68
Erasing: Tellme 39/68
Erasing: typo 40/68
Erasing: Coppermine 41/68
Shutting down psa-spamassassin service: [ OK ]
Shutting down psa-spamassassin service: [ OK ]
Delete spamassassin preferences from .qmail files for mailnames
Delete for "<emailaddress>.com"
Delete for "<emailaddress>.com"
/var/tmp/rpm-tmp.33885: line 212: /usr/bin/mysql: No such file or directory
error: %preun(psa-spamassassin-7.5.4-fc2.build75050824.12) scriptlet failed, exit status 127
/var/tmp/rpm-tmp.62240: line 86: : No such file or directory

/var/tmp/rpm-tmp.62240: line 86: : No such file or directory
WARNING!
/var/tmp/rpm-tmp.62240: line 112: : No such file or directory
During the webapp was NOT disabled. Unsupported operating system found some small problems(see log file: )
/var/tmp/rpm-tmp.62240: line 86: : No such file or directory

/var/tmp/rpm-tmp.62240: line 86: : No such file or directory
Continue...
/var/tmp/rpm-tmp.62240: line 86: : No such file or directory

Erasing: mod_webapp 42/68
Erasing: phpDig 43/68
Erasing: PPWSE 44/68
===> Updating /etc/psa/psa.conf...
===> Unregistering module
/var/tmp/rpm-tmp.62240: line 2035: /usr/bin/mysql: No such file or directory
===> Uninstalling database
/var/tmp/rpm-tmp.62240: line 2018: /usr/bin/mysql: No such file or directory
Erasing: cs-gs 45/68
Erasing: WebCalendar 46/68
Erasing: psa-api-cli 47/68
Erasing: mysql-compat 48/68
Erasing: WebShopmanager 49/68
Erasing: UebiMiau 50/68
===> Updating /etc/psa/psa.conf...
===> Unregistering module
/var/tmp/rpm-tmp.49325: line 2079: /usr/bin/mysql: No such file or directory
===> Unregistering service
Trying to unregister service psa-vpn... using /sbin/chkconfig
===> Uninstalling configuration files
===> Uninstalling database
/var/tmp/rpm-tmp.49325: line 2051: /usr/bin/mysql: No such file or directory
Erasing: psa-vpn 51/68
===> Updating /etc/psa/psa.conf...
===> Unregistering module
/var/tmp/rpm-tmp.2167: line 2034: /usr/bin/mysql: No such file or directory
===> Uninstalling database
/var/tmp/rpm-tmp.2167: line 2016: /usr/bin/mysql: No such file or directory
Erasing: psa-bf1942 52/68
===> Updating /etc/psa/psa.conf...


Trying to define super-server internet daemon type... xinetd
Trying to comment out old record for service smtp... done
Trying to set up record for service smtp... done
Trying to restart xinetd daemon... Trying to comment out old record for service smtps... done
Trying to set up record for service smtps... done
Trying to restart xinetd daemon... /var/tmp/rpm-tmp.8142: line 2467: /usr/bin/mysql: No such file or directory
error: %preun(psa-qmail-rblsmtpd-0.70-fc2.build75050824.12) scriptlet failed, exit status 127

 

[sector29]

<post 2>
.
.
Erasing: openbiblio 53/68
Erasing: phpMyFamily 54/68
warning: /usr/local/psa/version saved as /usr/local/psa/version.rpmsave
warning: /usr/local/psa/admin/conf/ssl.key/server.key saved as /usr/local/psa/admin/conf/ssl.key/server.key.rpmsave
warning: /usr/local/psa/admin/conf/ssl.crt/server.crt saved as /usr/local/psa/admin/conf/ssl.crt/server.crt.rpmsave
warning: /usr/local/psa/admin/conf/httpsd.conf saved as /usr/local/psa/admin/conf/httpsd.conf.rpmsave
Erasing: psa 55/68
Erasing: b2evolution 56/68
Erasing: gallery 57/68
Erasing: gtchat 58/68
Erasing: Owl 59/68
Erasing: WordPress 60/68
Erasing: AdvancedPoll 61/68
Erasing: psa-imp 62/68
Trying to start MySQL server...
ERROR while trying to start MySQL server
Check the error reason(see log file: /tmp/imp-4.0.3.log), fix and try again

Aborting...

error: %postun(psa-imp-4.0.3-fc2.build75050824.12) scriptlet failed, exit status 1
Erasing: psa-sbm 63/68
===> Unregistering module
===> Error while registering module in Plesk: can't access database.
error: %postun(psa-sbm-1.1-35) scriptlet failed, exit status 1
===> Updating /etc/psa/psa.conf...
===> Unregistering module
/var/tmp/rpm-tmp.9542: line 2047: /usr/bin/mysql: No such file or directory
===> Delete event handlers
/var/tmp/rpm-tmp.9542: line 2010: /usr/bin/mysql: No such file or directory
===> Stop monit
/var/tmp/rpm-tmp.9542: /usr/local/psa/admin/bin/modules/watchdog/stop-monit.php: /usr/local/psa/admin/bin/php: bad interpreter: No such file or directory
===> Uninstalling database
/var/tmp/rpm-tmp.9542: line 2031: /usr/bin/mysql: No such file or directory
Erasing: psa-watchdog 64/68
Erased: mysql 4.0.25-1.rhfc2.art.i386 psa-agent 1.3.5-75050824.12.noarch DocFAQ 1.71-7508.noarch php-mysql 4.3.10-2.4.i386 psa-turba 2.0.3-fc2.build75050824.12.noarch AutoIndex 1.5.3-7507.noarch osCommerce 2.2ms2-7509.noarch psa-fileserver 1.0.0-fc2.build75050824.12.i586 CSLH 2.12.2-7504.noarch psa-bu 7.5.4-fc2.build75050824.12.i586 xrms 1.19-7504.noarch bbclone 0.48-7508.noarch phpAds 2.0.5-7506.noarch psa-api-rpc 7.5.4-fc2.build75050824.12.noarch phpMoney 1.3-7510.noarch phpWiki 1.3.11-7508.noarch phpsurveyor 0.98-7510.noarch psa-migration-manager 7.5.4-fc2.build75050824.12.i586 sitebuilder_de_DE 1.0-0.i386 psa-passwd 3.0-fc2.build75050824.12.noarch perl-DBD-MySQL 2.9003-4.i386 phpBugTracker 1.19-7506.noarch psa-api-common 7.5.4-fc2.build75050824.12.noarch psa-kronolith 2.0.3-fc2.build75050824.12.noarch psa-mnemo 2.0.1-fc2.build75050824.12.noarch Mambo 4.5.2-7505.noarch SSHTerm 0.2.2-fc2.build75050824.12.noarch PostNuke 0.750-7505.noarch psa-manual-custom-skin-guide 7.5.4-fc2.build75050824.12.noarch psa-firewall 1.0.1-fc2.build75050824.12.i586 Sitebuilder 1.1.1-fc2.build050629.12.i386 frontpage 5.0-72psa.fc2.i586 phpBook 1.50-7507.noarch phpBB 2.0.17-7505.noarch psa-ingo 1.0.1-fc2.build75050824.12.noarch psa-horde 3.0.5-fc2.build75050824.12.noarch mysql-server 4.0.25-1.rhfc2.art.i386 pLog 1.0-7508.noarch TUTOS 1.88-7504.noarch Tellme 1.2-7507.noarch typo 3.8.0-7505.noarch Coppermine 1.3.3-7515.noarch psa-spamassassin 7.5.4-fc2.build75050824.12.i586 mod_webapp 4.1.29-41psa.fc2.i586 phpDig 1.85-7505.noarch PPWSE 1.1-fc2.build75050824.12.i586 cs-gs 1.2.2-fc2.build75050824.12.i586 WebCalendar 1.0-7504.noarch psa-api-cli 7.5.4-fc2.build75050824.12.noarch mysql-compat 4.0.25-1.rhfc2.art.i386 WebShopmanager 2.0-7506.noarch UebiMiau 2.7.8-7508.noarch psa-vpn 1.0.0-fc2.build75050824.12.i586 psa-bf1942 1.0.0-fc2.build75050824.12.i586 psa-qmail-rblsmtpd 0.70-fc2.build75050824.12.i586 psa-tomcat-configurator 7.5.4-fc2.build75050824.12.noarch openbiblio 0.5-7513.noarch phpMyFamily 1.4.1-7508.noarch psa 7.5.4-fc2.build75050824.12.i586 b2evolution 0.9.0.12-7505.noarch gallery 2.0-7516.noarch gtchat 0.93-7507.noarch Owl 0.80-7507.noarch WordPress 1.5.1-7509.noarch AdvancedPoll 2.03-7505.noarch psa-imp 4.0.3-fc2.build75050824.12.noarch psa-sbm 1.1-35.noarch psa-watchdog 1.0.0-fc2.build75050824.12.i586
Transaction(s) Complete
.
.
.
[root@<domain>]# yum update mysql
Gathering header information file(s) from server(s)
Server: Atomic Rocket Turtle - 2 - Atomic PSA-Compatible RPMS
Server: Fedora Core 2 - i386 - Base
Server: Fedora Core 2 - i386 - Released Updates
error: rpmdb: damaged header #53 retrieved -- skipping.
error: rpmdb: damaged header #241 retrieved -- skipping.
error: rpmdb: damaged header #253 retrieved -- skipping.
Finding updated packages
Downloading needed headers
Mambo-0-4.5.1a-1.noarch.h 100% |=========================| 1.9 kB 00:00
PostNuke-0-0.750-1.noarch 100% |=========================| 1.8 kB 00:00
Cannot find any package matching mysql available to be updated.
No actions to take
[root@<domain>]# service mysqld start
mysqld: unrecognized service
[root@<domain>]# yum install mysql
Gathering header information file(s) from server(s)
Server: Atomic Rocket Turtle - 2 - Atomic PSA-Compatible RPMS
Server: Fedora Core 2 - i386 - Base
Server: Fedora Core 2 - i386 - Released Updates
error: rpmdb: damaged header #53 retrieved -- skipping.
error: rpmdb: damaged header #241 retrieved -- skipping.
error: rpmdb: damaged header #253 retrieved -- skipping.
Finding updated packages
Downloading needed headers
Resolving dependencies
..Dependencies resolved
I will do the following:
[install: mysql 4.0.25-1.rhfc2.art.i386]
I will install/upgrade these to satisfy the dependencies:
[deps: perl-DBD-MySQL 2.9003-4.i386]
[deps: mysql-compat 4.0.25-1.rhfc2.art.i386]
Is this ok [y/N]: y
Downloading Packages
Getting perl-DBD-MySQL-2.9003-4.i386.rpm
perl-DBD-MySQL-2.9003-4.i 100% |=========================| 111 kB 00:00
Running test transaction:
Test transaction complete, Success!
mysql-compat 100 % done 1/3
perl-DBD-MySQL 100 % done 2/3
mysql 100 % done 3/3
Installed: mysql 4.0.25-1.rhfc2.art.i386
Dep Installed: perl-DBD-MySQL 2.9003-4.i386 mysql-compat 4.0.25-1.rhfc2.art.i386
Transaction(s) Complete
[root@<domain>]# service mysqld start
mysqld: unrecognized service
[root@<domain>]# service mysqld start
mysqld: unrecognized service
[root@<domain>]# yum install php
Gathering header information file(s) from server(s)
Server: Atomic Rocket Turtle - 2 - Atomic PSA-Compatible RPMS
Server: Fedora Core 2 - i386 - Base
Server: Fedora Core 2 - i386 - Released Updates
error: rpmdb: damaged header #53 retrieved -- skipping.
error: rpmdb: damaged header #241 retrieved -- skipping.
error: rpmdb: damaged header #253 retrieved -- skipping.
Finding updated packages
Downloading needed headers
Resolving dependencies
.Dependencies resolved
I will do the following:
[update: php 4.3.11-8.rhfc2.art.i386]
I will install/upgrade these to satisfy the dependencies:
[deps: php-mbstring 4.3.11-8.rhfc2.art.i386]
[deps: php-domxml 4.3.11-8.rhfc2.art.i386]
[deps: php-pgsql 4.3.11-8.rhfc2.art.i386]
[deps: php-imap 4.3.11-8.rhfc2.art.i386]
Is this ok [y/N]: y
Downloading Packages
Getting php-mbstring-4.3.11-8.rhfc2.art.i386.rpm
php-mbstring-4.3.11-8.rhf 100% |=========================| 1.1 MB 00:07
Getting php-domxml-4.3.11-8.rhfc2.art.i386.rpm
php-domxml-4.3.11-8.rhfc2 100% |=========================| 114 kB 00:00
Getting php-pgsql-4.3.11-8.rhfc2.art.i386.rpm
php-pgsql-4.3.11-8.rhfc2. 100% |=========================| 110 kB 00:00
Getting php-4.3.11-8.rhfc2.art.i386.rpm
php-4.3.11-8.rhfc2.art.i3 100% |=========================| 3.2 MB 00:24
Getting php-imap-4.3.11-8.rhfc2.art.i386.rpm
php-imap-4.3.11-8.rhfc2.a 100% |=========================| 488 kB 00:03
Running test transaction:
Test transaction complete, Success!
php-imap 100 % done 1/10
warning: /etc/httpd/conf.d/php.conf saved as /etc/httpd/conf.d/php.conf.rpmsave
warning: /etc/php.ini created as /etc/php.ini.rpmnew
php 100 % done 2/10
php-pgsql 100 % done 3/10
php-domxml 100 % done 4/10
php-mbstring 100 % done 5/10
Completing update for php-mbstring - 6/10
Completing update for php-domxml - 7/10
Completing update for php-pgsql - 8/10
Completing update for php - 9/10
Completing update for php-imap - 10/10
Updated: php 4.3.11-8.rhfc2.art.i386
Dep Installed: php-mbstring 4.3.11-8.rhfc2.art.i386 php-domxml 4.3.11-8.rhfc2.art.i386 php-pgsql 4.3.11-8.rhfc2.art.i386 php-imap 4.3.11-8.rhfc2.art.i386
Transaction(s) Complete

 

[jamesyeeoc]

Yeah, ummm, do you have a recent server backup which you can use to do a full restore? That would be a whole lot easier than having to reinstall basically the entire list of all the dependencies which were removed (basically just about everything except the OS).

 

[CBiLL]

if you were upgrading from 3 to 4, did you do a privilage table fix?

Bill

 

[jamesyeeoc]

He's beyond the priv fix.

It appears that when he uninstalled mysql, yum also removed all other packages which depended on it, so at this point, (if you look at the list of deps removed), he is basically starting out with a fresh server and would have to install everything from scratch, or (as I posted) use a recent backup to do a full restore.

 

[sector29]

My understanging is that backups are not automatic on my setup and I don't want to go back too far.

I'm going to download my docs and mysql tables and indexes and see if i can get the server reset.

Can someone explain fixing privaleges. If I get the server fixed I'm going to try it again. I can live without PHP5 for now but having a current version of mysql would be a nice tradeoff.

What does RPM stand for?

 

[jamesyeeoc]

RPM = Redhat Package Manager, a way to 'package' and distribute software compiled for a specific Linux distribution.

Privilege Tables Fix - is a fix utility when upgrading from mySQL 3.x to 4.x, I don't know what is needed if you are upgrading to 5.x (have not crossed that bridge myself yet)

For future, you should ALWAYS do a full backup BEFORE doing any updating or upgrading. It will save you much headaches and time when or if something goes wrong.