mysql upgrade issue

Sniffty Dugen

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Dec 27, 2017, 4:04:13 PM12/27/17

to security-onion

Patched a sensor today and have run into this mysql upgrade issue. Can anyone offer some advice on how to fix this without having to redo the entire sensor? most of the suggestions Ive seen say apt-get remove --purge mysql-server, if I do that of course every dependency will get removed with it.

any help is appreciated

sudo soup yields

Setting up mysql-server-5.5 (5.5.58-0ubuntu0.14.04.1) ...
start: Job failed to start
invoke-rc.d: initscript mysql, action "start" failed.
dpkg: error processing package 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 package mysql-server (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of securityonion-elsa:
securityonion-elsa depends on mysql-server; however:
Package mysql-server is not configured yet.

dpkg: error processing package securityonion-elsa (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of securityonion-iso:
securityonion-iso depends on securityonion-elsa; however:
Package securityonion-elsa is not configured yet.

dpkg: error processing package securityonion-iso (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of securityonion-elsa-extras:
securityonion-elsa-extras depends on securityonion-elsa; however:
Package securitNo apport report written because the error message indicates its a followup error from a previous failure.
No apport report written because the error message indicates its a followup error from a previous failure.
No apport report written because MaxReports is reached already
No apport report written because MaxReports is reached already
No apport report written because MaxReports is reached already
yonion-elsa is not configured yet.

dpkg: error processing package securityonion-elsa-extras (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of securityonion-squert:
securityonion-squert depends on mysql-server; however:
Package mysql-server is not configured yet.

dpkg: error processing package securityonion-squert (--configure):
dependency problems - leaving unconfigured
Errors were encountered while processing:
mysql-server-5.5
mysql-server
securityonion-elsa
securityonion-iso
securityonion-elsa-extras
securityonion-squert

sudo dpkg --configure mysql-server

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 package mysql-server (--configure):
dependency problems - leaving unconfigured
Errors were encountered while processing:
mysql-server

Doug Burks

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Dec 29, 2017, 3:31:39 PM12/29/17

to securit...@googlegroups.com

Hi Sniffty,

Please try the following and if it doesn't help, please include all
output in your reply:

sudo service nsm stop
sudo service syslog-ng stop
sudo service apache2 stop
sudo pkill autossh
sudo pkill perl
sudo apt update
sudo apt dist-upgrade

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Sniffty Dugen

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Jan 2, 2018, 9:29:05 AM1/2/18

to security-onion

Doug

No luck, here is the output

mome:~$ sudo service nsm stop
Stopping: HIDS
* stopping: ossec_agent (sguil) [ OK ]
Stopping: Bro
stopping mome-eth3-1 ...
stopping mome-eth3-2 ...
stopping proxy ...
stopping manager ...
Stopping: mome-eth3
* stopping: netsniff-ng (full packet data) [ OK ]
* stopping: pcap_agent (sguil) [ OK ]
* stopping: snort_agent-1 (sguil) [ OK ]
* stopping: snort_agent-2 (sguil) [ OK ]
* stopping: snort-1 (alert data) [ OK ]
* stopping: snort-2 (alert data) [ OK ]
* stopping: barnyard2-1 (spooler, unified2 format) [ OK ]
* stopping: barnyard2-2 (spooler, unified2 format) [ OK ]
mome:~$ sudo service syslog-ng stop
* Stopping system logging syslog-ng [ OK ]
mome:~$ sudo service apache2 stop
* Stopping web server apache2 *
mome:~$ sudo pkill autossh
mome:~$ sudo pkill perl

mome:~$ sudo apt dist-upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages were automatically installed and are no longer required:
gir1.2-json-1.0 gir1.2-timezonemap-1.0 gir1.2-xkl-1.0 lame libgeoip-dev
libjson-c-dev libmono-accessibility2.0-cil libmono-corlib2.0-cil
libmono-data-tds2.0-cil libmono-i18n-west2.0-cil libmono-messaging2.0-cil
libmono-posix2.0-cil libmono-security2.0-cil libmono-sharpzip2.84-cil
libmono-sqlite2.0-cil libmono-system-data-linq2.0-cil
libmono-system-data2.0-cil libmono-system-messaging2.0-cil
libmono-system-runtime2.0-cil libmono-system-web2.0-cil
libmono-system2.0-cil libmono-wcf3.0a-cil libmono-webbrowser2.0-cil
libmono-winforms2.0-cil libmono2.0-cil libmp3lame0 librecode0
libtimezonemap1 linux-headers-4.4.0-59 linux-headers-4.4.0-72
linux-headers-4.4.0-87 linux-headers-4.4.0-87-generic
linux-image-4.4.0-87-generic linux-image-extra-4.4.0-87-generic php5-sqlite
python3-httplib2 python3-psycopg2 recode securityonion-ndpi sqlite3 xplico
Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
6 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 (5.5.58-0ubuntu0.14.04.1) ...
start: Job failed to start
invoke-rc.d: initscript mysql, action "start" failed.
dpkg: error processing package 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 package mysql-server (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of securityonion-elsa:
securityonion-elsa depends on mysql-server; however:
Package mysql-server is not configured yet.

dpkg: error processing package securityonion-elsa (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of securityonion-iso:
securityonion-iso depends on securityonion-elsa; however:
Package securityonion-elsa is not configured yet.

dpkg: error processing package securityonion-iso (--configure):
dependency problems - leaving unconfigured

dpkg: dependency probleNo apport report written because the error message indicates its a followup error from a previous failure.

No apport report written because the error message indicates its a followup error from a previous failure.
No apport report written because MaxReports is reached already
No apport report written because MaxReports is reached already
No apport report written because MaxReports is reached already

ms prevent configuration of securityonion-elsa-extras:
securityonion-elsa-extras depends on securityonion-elsa; however:

Package securityonion-elsa is not configured yet.

dpkg: error processing package securityonion-elsa-extras (--configure):

dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of securityonion-squert:
securityonion-squert depends on mysql-server; however:
Package mysql-server is not configured yet.

dpkg: error processing package securityonion-squert (--configure):
dependency problems - leaving unconfigured
Errors were encountered while processing:
mysql-server-5.5
mysql-server
securityonion-elsa
securityonion-iso
securityonion-elsa-extras
securityonion-squert

E: Sub-process /usr/bin/dpkg returned an error code (1)

Doug Burks

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Jan 3, 2018, 6:35:51 AM1/3/18

to securit...@googlegroups.com

Please try the following and if it doesn't help, please include all
output in your reply:

sudo service nsm stop
sudo service syslog-ng stop
sudo service apache2 stop
sudo pkill autossh
sudo pkill perl
sudo apt update

sudo apt-get -f install

Also check for additional clues in /var/log/mysql/.

Sniffty Dugen

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Jan 3, 2018, 5:39:41 PM1/3/18

to security-onion

OK, added the following line into /etc/mysql/my.cnf
innodb_force_recovery = 4

which allowed me to start mysql and continue with the mysql update. Which completed successfully.

The underlying issue is corrupt data in the syslog_data db. Here is to hoping a repair works.

Thanks for the help Doug.

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