[debian-mysql] Bug#805828: mysql-server-5.6: upgrade didn't work, package unusable, mysql does not start

jpp jp.pozzi at izzop.net
Sun Nov 22 21:02:05 UTC 2015

Package: mysql-server-5.6
Version: 5.6.27-2
Severity: critical
Justification: causes serious data loss


I am using the "unstable" release and after the previous update Mysql is
The configuration files where updated and the result is an unusable database.
Mysql won't start giving me stranges messages.
The /var/lib/mysql is a symlinj to another location on another disk.
I saw that some configuration options where not ok :
innodb_data_home_dir =
innodb_data_file_path =
No directory for innodb_data_home_dir ?
The "bind address" which was "" has disapeared.
I try some workaround. If I use :
innodb_data_home_dir = /var/lib/mysql/
innodb_data_file_path = ibdata1:1024M;ibdata2:1024M:autoextend
I get messages complaining on system error reading files.

After a while I delete all "ib...." files and relaunch the service with no
the "ib..." files were recreated but the error.log mentionned that it can bind
to this
address ( and asking if another mysql process was running (this is
not the case).

I try to use a specific address "bind" and mysql does not start
with messages :

2015-11-22 21:53:53 4936 [Note] InnoDB: Waiting for purge to start
2015-11-22 21:53:53 4936 [Note] InnoDB: 5.6.27 started; log sequence number
2015-11-22 21:53:53 4936 [Note] Recovering after a crash using /var/log/mysql
2015-11-22 21:53:53 4936 [Note] Starting crash recovery...
2015-11-22 21:53:53 4936 [Note] Crash recovery finished.
2015-11-22 21:53:53 4936 [Note] Server hostname (bind-address): '';
port: 3306
2015-11-22 21:53:53 4936 [Note]   - '' resolves to '';
2015-11-22 21:53:53 4936 [Note] Server socket created on IP: ''.
2015-11-22 21:53:53 4936 [ERROR] Fatal error: Can't open and lock privilege
tables: Table 'mysql.user' doesn't exist

The upgrade was not successful and I get a fully crashed database.



PS : I save some distinct error logs.

-- System Information:
Debian Release: stretch/sid
  APT prefers testing-updates
  APT policy: (500, 'testing-updates'), (500, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 4.3.0-x (SMP w/8 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages mysql-server-5.6 depends on:
ii  adduser                3.113+nmu3
ii  debconf [debconf-2.0]  1.5.58
ii  init-system-helpers    1.24
ii  initscripts            2.88dsf-59.2
ii  libaio1                0.3.110-2
ii  libc6                  2.19-22
ii  libdbi-perl            1.634-1
ii  libgcc1                1:5.2.1-23
ii  libstdc++6             5.2.1-23
ii  libwrap0               7.6.q-25
ii  lsb-base               9.20150917
ii  mysql-client-5.6       5.6.27-2
ii  mysql-common           5.6.27-2
ii  mysql-server-core-5.6  5.6.27-2
ii  passwd                 1:4.2-3.1
ii  perl                   5.20.2-6
ii  psmisc                 22.21-2.1
ii  zlib1g                 1:1.2.8.dfsg-2+b1

Versions of packages mysql-server-5.6 recommends:
ii  libhtml-template-perl  2.95-2

Versions of packages mysql-server-5.6 suggests:
ii  bsd-mailx [mailx]  8.1.2-0.20150408cvs-1
pn  tinyca             <none>

-- Configuration Files:
/etc/logcheck/ignore.d.paranoid/mysql-server-5_6 [Errno 13] Permission denied: u'/etc/logcheck/ignore.d.paranoid/mysql-server-5_6'
/etc/logcheck/ignore.d.server/mysql-server-5_6 [Errno 13] Permission denied: u'/etc/logcheck/ignore.d.server/mysql-server-5_6'
/etc/logcheck/ignore.d.workstation/mysql-server-5_6 [Errno 13] Permission denied: u'/etc/logcheck/ignore.d.workstation/mysql-server-5_6'
/etc/mysql/mysql.cnf [Errno 2] No such file or directory: u'/etc/mysql/mysql.cnf'
/etc/mysql/mysql.conf.d/mysqld.cnf changed:
socket		= /var/run/mysqld/mysqld.sock
nice		= 0
user		= mysql
pid-file	= /var/run/mysqld/mysqld.pid
socket		= /var/run/mysqld/mysqld.sock
basedir		= /usr
datadir		= /var/lib/mysql
tmpdir		= /tmp
lc-messages-dir	= /usr/share/mysql
port		= 3306
bind-address	=
key_buffer_size		= 16M
max_allowed_packet	= 16M
thread_stack		= 192K
thread_cache_size       = 8
myisam-recover         = BACKUP
max_connections        = 16
query_cache_limit	= 1M
query_cache_size        = 16M
general_log_file        = /var/log/mysql/mysql.log
general_log             = 1
log_error = /var/log/mysql/error.log
server-id		= 1
log_bin			= /var/log/mysql/mysql-bin.log
expire_logs_days	= 10
max_binlog_size   	= 100M
innodb_data_home_dir = /var/lib/mysql
innodb_data_file_path = ibdata1:1024M;ibdata2:1024M:autoextend
innodb_log_file_size = 128M

-- debconf information excluded

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