Getting mySQL server back on Ubuntu 12.04

**lads** · June 6th, 2012

Dear all,

I found out today that the upgrade to Ubuntu 12.04 send out mySQL to the void. I immediately tried to get it back but got an error:

Code:

$ sudo apt-get install mysql-server
[sudo] password for desousa: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  mysql-server-5.5 mysql-server-core-5.5
Suggested packages:
  tinyca
The following NEW packages will be installed:
  mysql-server mysql-server-5.5 mysql-server-core-5.5
0 upgraded, 3 newly installed, 0 to remove and 26 not upgraded.
Need to get 14.9 MB of archives.
After this operation, 52.9 MB of additional disk space will be used.
Do you want to continue [Y/n]? Y
Get:1 http://de.archive.ubuntu.com/ubuntu/ precise/main mysql-server-core-5.5 amd64 5.5.22-0ubuntu1 [6,022 kB]
Get:2 http://de.archive.ubuntu.com/ubuntu/ precise/main mysql-server-5.5 amd64 5.5.22-0ubuntu1 [8,816 kB]
Get:3 http://de.archive.ubuntu.com/ubuntu/ precise/main mysql-server all 5.5.22-0ubuntu1 [11.8 kB]
Fetched 14.9 MB in 2s (4,960 kB/s)       
Preconfiguring packages ...
Selecting previously unselected package mysql-server-core-5.5.
(Reading database ... 412919 files and directories currently installed.)
Unpacking mysql-server-core-5.5 (from .../mysql-server-core-5.5_5.5.22-0ubuntu1_amd64.deb) ...
Selecting previously unselected package mysql-server-5.5.
Unpacking mysql-server-5.5 (from .../mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb) ...
dpkg: error processing /var/cache/apt/archives/mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb (--unpack):
 trying to overwrite '/usr/lib/mysql/plugin/ha_example.so', which is also in package libmysqlclient-dev 5.5.23-1~dotdeb.0
Selecting previously unselected package mysql-server.
Unpacking mysql-server (from .../mysql-server_5.5.22-0ubuntu1_all.deb) ...
Processing triggers for man-db ...
Processing triggers for ureadahead ...
ureadahead will be reprofiled on next reboot
Errors were encountered while processing:
 /var/cache/apt/archives/mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

After this mySQL is not available:

Code:

$ sudo netstat -tap | grep mysql
$ sudo /etc/init.d/mysql restart
sudo: /etc/init.d/mysql: command not found

The first web search results pointed to an issue with the root password. I tried to reconfigure:

Code:

$ sudo dpkg-reconfigure mysql-server
/usr/sbin/dpkg-reconfigure: mysql-server is broken or not fully installed

After some more duckduckgoing I found a reference to the old packages disturbing the new installation. Indeed some old packages were still there:

Code:

$ dpkg --get-selections | grep mysql
gambas2-gb-db-mysql				install
libdbd-mysql-perl				install
libmysqlclient-dev				install
libmysqlclient16				install
libmysqlclient18				install
libqt4-sql-mysql				install
mysql-admin					deinstall
mysql-client-5.5				install
mysql-client-core-5.5				install
mysql-common					install
mysql-query-browser				deinstall
mysql-server					install
mysql-server-5.1				deinstall
mysql-server-core-5.5				install
mysql-workbench					install
mysql-workbench-data				install
python-mysql.connector				install

$ sudo dpkg --purge mysql-admin mysql-query-browser mysql-server-5.1
(Reading database ... 413009 files and directories currently installed.)
Removing mysql-admin ...
Purging configuration files for mysql-admin ...
Removing mysql-query-browser ...
Purging configuration files for mysql-query-browser ...
Removing mysql-server-5.1 ...
Purging configuration files for mysql-server-5.1 ...
Processing triggers for ureadahead ...

$ dpkg --get-selections | grep mysql
gambas2-gb-db-mysql				install
libdbd-mysql-perl				install
libmysqlclient-dev				install
libmysqlclient16				install
libmysqlclient18				install
libqt4-sql-mysql				install
mysql-client-5.5				install
mysql-client-core-5.5				install
mysql-common					install
mysql-server-core-5.5				install
mysql-workbench					install
mysql-workbench-data				install
python-mysql.connector				install

Still, after purging the old packages I'm getting the same error as above. What is going wrong here? Is mySQL supposed to run on 12.04? If yes how can I install it?

Thanks.

**lads** · June 7th, 2012

There's a new development today. As I tried to run the morning upgrade I got this:

Code:

$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree       
Reading state information... Done
You might want to run 'apt-get -f install' to correct these.
The following packages have unmet dependencies:
 mysql-server : Depends: mysql-server-5.5 but it is not installed
E: Unmet dependencies. Try using -f.

So I did as it suggested:

Code:

$ sudo apt-get -f install
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Correcting dependencies... Done
The following extra packages will be installed:
  mysql-server-5.5
Suggested packages:
  tinyca
The following NEW packages will be installed:
  mysql-server-5.5
0 upgraded, 1 newly installed, 0 to remove and 55 not upgraded.
1 not fully installed or removed.
Need to get 0 B/8,816 kB of archives.
After this operation, 32.6 MB of additional disk space will be used.
Do you want to continue [Y/n]? Y
Preconfiguring packages ...
(Reading database ... 413000 files and directories currently installed.)
Unpacking mysql-server-5.5 (from .../mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb) ...
dpkg: error processing /var/cache/apt/archives/mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb (--unpack):
 trying to overwrite '/usr/lib/mysql/plugin/ha_example.so', which is also in package libmysqlclient-dev 5.5.23-1~dotdeb.0
Processing triggers for ureadahead ...
ureadahead will be reprofiled on next reboot
Processing triggers for man-db ...
Errors were encountered while processing:
 /var/cache/apt/archives/mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

So it seems mysql-server has even embroiled the upgrade. Any clues on how to fix this?

Thank you.

**lads** · June 8th, 2012

Today I tried to install mySQL with aptitude to see if something would come up in the log:

Code:

$ sudo aptitude install mysql-server
The following NEW packages will be installed:
  mysql-server mysql-server-5.5{a} 
0 packages upgraded, 2 newly installed, 0 to remove and 16 not upgraded.
Need to get 0 B/8,828 kB of archives. After unpacking 32.8 MB will be used.
Do you want to continue? [Y/n/?] Y
Preconfiguring packages ...              
(Reading database ... 413046 files and directories currently installed.)
Unpacking mysql-server-5.5 (from .../mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb) ...
dpkg: error processing /var/cache/apt/archives/mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb (--unpack):
 trying to overwrite '/usr/lib/mysql/plugin/ha_example.so', which is also in package libmysqlclient-dev 5.5.23-1~dotdeb.0
No apport report written because MaxReports is reached already
                                                              Selecting previously unselected package mysql-server.
Unpacking mysql-server (from .../mysql-server_5.5.22-0ubuntu1_all.deb) ...
Processing triggers for ureadahead ...
ureadahead will be reprofiled on next reboot
Processing triggers for man-db ...
Errors were encountered while processing:
 /var/cache/apt/archives/mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
A package failed to install.  Trying to recover:
dpkg: dependency problems prevent configuration of mysql-server:
 mysql-server depends on mysql-server-5.5; however:
  Package mysql-server-5.5 is not installed.
dpkg: error processing mysql-server (--configure):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 mysql-server
                                         
Current status: 1 broken [+1].

$ cat /var/log/aptitude
Aptitude 0.6.6: log report
Fri, Jun  8 2012 11:26:43 +0200

IMPORTANT: this log only lists intended actions; actions which fail due to
dpkg problems may not be completed.

Will install 2 packages, and remove 0 packages.
32.8 MB of disk space will be used
===============================================================================
[HOLD, DEPENDENCIES] libcairo-gobject2:amd64
[HOLD, DEPENDENCIES] libcairo-gobject2:i386
[HOLD, DEPENDENCIES] libcairo-script-interpreter2:amd64
[HOLD, DEPENDENCIES] libcairo2:i386
[HOLD, DEPENDENCIES] libcairo2-dev:amd64
[HOLD, DEPENDENCIES] libgdal1-1.7.0:amd64
[HOLD, DEPENDENCIES] printer-driver-ptouch:amd64
[HOLD, DEPENDENCIES] rpcbind:amd64
[INSTALL, DEPENDENCIES] mysql-server-5.5:amd64
[HOLD] libcairo2:amd64
[HOLD] libgdal1:amd64
[HOLD] ptouch-driver:amd64
[HOLD] python-cupshelpers:amd64
[HOLD] software-center:amd64
[HOLD] system-config-printer-common:amd64
[HOLD] system-config-printer-gnome:amd64
[HOLD] system-config-printer-udev:amd64
[INSTALL] mysql-server:amd64
===============================================================================

Log complete.

It doesn't say much to me. Any clues?

Thank you.

**worthspending** · June 9th, 2012

I did a fresh install on three local machine directly from CD with no problem. Leased a dedicated server from 1and1 running Ubuntu 12.04 LTS and had the same problems as you have described. I will keep you in the loop if I figure something out. This is really turning into a pain...

**worthspending** · June 9th, 2012

I removed everything related to mysql-server.

sudo apt-get remove mysql-server

physically removed all of the files from the following search
find / -name 'mysql*'

then, I uninstalled apparmor.
sudo apt-get remove apparmor

then, reinstall mysql-server
sudo apt-get install mysql-server

it worked and started up. rebooted and it was still working. tried to reinstall apparmor and got the following:

Setting up apparmor (2.7.102-0ubuntu3) ...
* Starting AppArmor profiles Skipping profile in /etc/apparmor.d/disable: usr.sbin.rsyslogd
AppArmor parser error for /etc/apparmor.d/usr.sbin.mysqld in /etc/apparmor.d/tunables/global at line 17: Could not open 'tunables/proc'
AppArmor parser error for /etc/apparmor.d/sbin.dhclient in /etc/apparmor.d/tunables/global at line 17: Could not open 'tunables/proc'
AppArmor parser error for /etc/apparmor.d/usr.sbin.tcpdump in /etc/apparmor.d/tunables/global at line 17: Could not open 'tunables/proc'
[fail]
invoke-rc.d: initscript apparmor, action "start" failed.
* Reloading AppArmor profiles Skipping profile in /etc/apparmor.d/disable: usr.sbin.rsyslogd
AppArmor parser error for /etc/apparmor.d/sbin.dhclient in /etc/apparmor.d/tunables/global at line 17: Could not open 'tunables/proc'
AppArmor parser error for /etc/apparmor.d/usr.sbin.mysqld in /etc/apparmor.d/tunables/global at line 17: Could not open 'tunables/proc'
AppArmor parser error for /etc/apparmor.d/usr.sbin.tcpdump in /etc/apparmor.d/tunables/global at line 17: Could not open 'tunables/proc'
invoke-rc.d: initscript apparmor, action "reload" failed.

seems like some files are jacked up. hope that helps!!

**lads** · June 11th, 2012

Thank you for the reply worthspending. I tried it the way you suggested but the end result is the same. The log goes below.

Thank you anyway.

Code:

$ sudo rm -r /usr/lib/mysql
$ sudo rm -r /usr/sbin/mysqld
$ sudo rm -r /usr/share/mysql
$ sudo rm -r /usr/bin/mysqlrepair
$ sudo rm -r /usr/bin/mysql_config
$ sudo rm -r /usr/bin/mysqldumpslow
$ sudo rm -r /usr/bin/mysqlbug
$ sudo rm -r /usr/bin/mysql_plugin
$ sudo rm -r /usr/bin/mysqlslap
$ sudo rm -r /usr/bin/mysqlcheck
$ sudo rm -r /usr/bin/mysqlshow
$ sudo rm -r /usr/bin/mysqldump
$ sudo rm -r /usr/bin/mysqlaccess
$ sudo rm -r /usr/bin/mysqlanalyze
$ sudo rm -r /usr/bin/mysql_install_db
$ sudo rm -r /usr/bin/mysqladmin
$ sudo rm -r /usr/bin/mysql_find_rows
$ sudo rm -r /usr/bin/mysql_upgrade
$ sudo rm -r /usr/bin/mysqlreport
$ sudo rm -r /usr/bin/mysql_fix_extensions
$ sudo rm -r /usr/bin/mysql_client_test
$ sudo rm -r /usr/bin/mysql
$ sudo rm -r /usr/bin/mysqlimport
$ sudo rm -r /usr/bin/mysql-workbench
$ sudo rm -r /usr/bin/mysqloptimize
$ sudo rm -r /usr/bin/mysql_waitpid
$ sudo rm -r /usr/include/mysql

$ sudo apt-get remove apparmor
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages will be REMOVED:
  apparmor apparmor-utils
0 upgraded, 0 newly installed, 2 to remove and 21 not upgraded.
After this operation, 1,607 kB disk space will be freed.
Do you want to continue [Y/n]? Y
(Reading database ... 413043 files and directories currently installed.)
Removing apparmor-utils ...
Removing apparmor ...
 * Clearing AppArmor profiles cache                                                                                                                                             [ OK ] 
All profile caches have been cleared, but no profiles have been unloaded.
Unloading profiles will leave already running processes permanently
unconfined, which can lead to unexpected situations.

To set a process to complain mode, use the command line tool
'aa-complain'. To really tear down all profiles, run the init script
with the 'teardown' option."
Processing triggers for man-db ...
Processing triggers for ureadahead ...
ureadahead will be reprofiled on next reboot

desousa@CRTE-LDS-15461:~$ sudo apt-get install mysql-server
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  mysql-server-5.5
Suggested packages:
  tinyca
The following NEW packages will be installed:
  mysql-server mysql-server-5.5
0 upgraded, 2 newly installed, 0 to remove and 21 not upgraded.
Need to get 0 B/8,828 kB of archives.
After this operation, 32.8 MB of additional disk space will be used.
Do you want to continue [Y/n]? Y
Preconfiguring packages ...
(Reading database ... 412972 files and directories currently installed.)
Unpacking mysql-server-5.5 (from .../mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb) ...
dpkg: error processing /var/cache/apt/archives/mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb (--unpack):
 trying to overwrite '/usr/lib/mysql/plugin/ha_example.so', which is also in package libmysqlclient-dev 5.5.23-1~dotdeb.0
Selecting previously unselected package mysql-server.
Unpacking mysql-server (from .../mysql-server_5.5.22-0ubuntu1_all.deb) ...
Processing triggers for ureadahead ...
Processing triggers for man-db ...
Errors were encountered while processing:
 /var/cache/apt/archives/mysql-server-5.5_5.5.22-0ubuntu1_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

**lads** · June 12th, 2012

At AskUbuntu this is being diagnosed as a conflict with package(s) installed from dotdeb.org. Indeed I had PHP installed from there, but no clear way how to fix it yet.

Code:

$ sudo cat /etc/apt/sources.list | grep dotdeb.org 
# deb php53.dotdeb.org stable all # disabled on upgrade to precise 
# deb-src php53.dotdeb.org stable all # disabled on upgrade to precise 

$ sudo aptitude search "?installed?origin(dotdeb.org)" 

$ sudo aptitude search "?installed?origin(php53.dotdeb.org)"

Any more clues welcome.

**lads** · June 13th, 2012

Today I downloaded the rpm from the mySQL website and tried to install it directly with alien. The result is essentially the same:

Code:

$ sudo alien -i MySQL-server-5.5.25-1.linux2.6.x86_64.rpm --scripts
	dpkg --no-force-overwrite -i mysql-server_5.5.25-2_amd64.deb
Selecting previously unselected package mysql-server.
(Reading database ... 409708 files and directories currently installed.)
Unpacking mysql-server (from mysql-server_5.5.25-2_amd64.deb) ...
dpkg: error processing mysql-server_5.5.25-2_amd64.deb (--install):
 trying to overwrite '/usr/sbin/mysqld', which is also in package mysql-server-core-5.5 5.5.24-0ubuntu0.12.04.1
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
Errors were encountered while processing:
 mysql-server_5.5.25-2_amd64.deb
Unable to install at /usr/share/perl5/Alien/Package/Deb.pm line 92, <GETPERMS> line 192.
	find MySQL-server-5.5.25 -type d -exec chmod 755 {} ;
	rm -rf MySQL-server-5.5.25

The message is still quite cryptic and I don't see here any complain about dotdeb.org.

Shouldn't this be filed as a bug?

**lads** · June 13th, 2012

Finally I managed to install mysql server using the -f argument in the apt-get command:

Code:

apt-get install -f mysql-server

Thanks to a tip at AskUbuntu.

**nirwanadhiatma** · July 1st, 2012

Originally Posted by lads

Finally I managed to install mysql server using the -f argument in the apt-get command:

Code:

apt-get install -f mysql-server

Thanks to a tip at AskUbuntu.

i've tried your method but it didn't work either :

root@linux:~# apt-get install -f mysql-server
Reading package lists... Done
Building dependency tree
Reading state information... Done
mysql-server is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
2 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Do you want to continue [Y/n]? y
Setting up mysql-server-5.5 (5.5.24-0ubuntu0.12.04.1) ...
start: Job failed to start
invoke-rc.d: initscript mysql, action "start" failed.
dpkg: error processing mysql-server-5.5 (--configure):
subprocess installed post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of mysql-server:
mysql-server depends on mysql-server-5.5; however:
Package mysql-server-5.5 is not configured yet.
dpkg: error processing mysql-server (--configure):
dependency problems - leaving unconfigured
No apport report written because the error message indicates its a followup error from a previous failure.
Errors were encountered while processing:
mysql-server-5.5
mysql-server
E: Sub-process /usr/bin/dpkg returned an error code (1)

Please help me

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