MySQL 5.6.19, for Debian Wheezy

June 10, 2014 · Guillaume Plessis

MySQL 5.6.19 has been released on May 30th, 2014, fixing various bugs.

Please read the full Changelog fore more details.

The corresponding packages are now available for Debian 7 “Wheezy”, on both amd64 and i386 architectures.

nyro June 10, 2014
After upgrading some server, I have 3 on 4 of them who got the error: cp: cannot overwrite directory `/var/lib/mysql-upgrade/DATADIR.link/mysql’ with non-directory
The mysql seems to be updated, but Aptitude still thinks mysql-server-5.6 needs to be updated.
Here is the full output: #aptitude full-upgrade The following packages will be upgraded: mysql-server-5.6 1 packages upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/14.8 MB of archives. After unpacking 8,192 B will be used. Do you want to continue? [Y/n/?] y Reading changelogs… Done Preconfiguring packages … (Reading database … 38382 files and directories currently installed.) Preparing to replace mysql-server-5.6 5.6.17-1~~dotdeb.1 (using …/mysql-server-5.6_5.6.19-1~~dotdeb.1_amd64.deb) … [ ok ] Stopping MySQL database server: mysqld. [ ok ] Stopping MySQL database server: mysqld. cp: cannot overwrite directory `/var/lib/mysql-upgrade/DATADIR.link/mysql’ with non-directory dpkg: error processing /var/cache/apt/archives/mysql-server-5.6_5.6.19-1dotdeb.1_amd64.deb (–unpack): subprocess new pre-installation script returned error exit status 1 [ ok ] Stopping MySQL database server: mysqld. [….] Starting MySQL database server: mysqldNo directory, logging in with HOME=/ . ok [info] Checking for tables which need an upgrade, are corrupt or were not closed cleanly.. [ ok ] Starting MySQL database server: mysqld already running. Errors were encountered while processing: /var/cache/apt/archives/mysql-server-5.6_5.6.19-1dotdeb.1_amd64.deb E: Sub-process /usr/bin/dpkg returned an error code (1) A package failed to install. Trying to recover:
- Nicolas Steinmetz June 14, 2014
  Hi,
  I got the same as /var/lib/mysql for me is a symlink to somewhere else on my server.
  I restored a real /var/lib/mysql directory and it almost worked :
  [….] Starting MySQL database server: mysqldPas de répertoire, connexion avec HOME=/
  Full output :
  root@cfl2013:# aptitude upgrade Les paquets suivants seront mis à jour :
  mysql-server-5.6 1 paquets mis à jour, 0 nouvellement installés, 0 à enlever et 0 non mis à jour. Il est nécessaire de télécharger 0 o/14,8 Mo d’archives. Après dépaquetage, 8 192 o seront utilisés. Voulez-vous continuer ? [Y/n/?] Préconfiguration des paquets…
  (Lecture de la base de données… 27059 fichiers et répertoires déjà installés.) Préparation du remplacement de mysql-server-5.6 5.6.17-1dotdeb.1 (en utilisant …/mysql-server-5.6_5.6.19-1dotdeb.1_amd64.deb) … [ ok ] Stopping MySQL database server: mysqld. [ ok ] Stopping MySQL database server: mysqld. Dépaquetage de la mise à jour de mysql-server-5.6 … Traitement des actions différées (« triggers ») pour « man-db »… Paramétrage de mysql-server-5.6 (5.6.19-1dotdeb.1) … [ ok ] Stopping MySQL database server: mysqld. [….] Starting MySQL database server: mysqldPas de répertoire, connexion avec HOME=/ [ .k [info] Checking for tables which need an upgrade, are corrupt or were not closed cleanly.. [ ok ] Starting MySQL database server: mysqld already running.
  État actuel : 0 paquet cassé [-1], 0 mise à jour restante [-1].
  Even removing and re-installing mysql-server-5.6 will lead to the same output.
  Let me know if you need more details !
  - Nicolas Steinmetz June 14, 2014
    I forgot to precise I’m on Debian Wheezy (7.5)
- Joe Auty August 12, 2014
  Nyro, did you ever figure out the cause of this? I’m having the exact same problem.
  - Nyro August 25, 2014
    Yes, I found out that was because I add a symlink for my mysql data directory.
    In order to solve it:
    1. Stop MySQL server
    2. Remove symlink
    3. Create new empty data dir
    4. Update MySQL package
    5. Restop MySQL (as the update might have update it)
    6. Re-add your symlink
    7. Start MySQL
    - Joe Auty August 26, 2014
      Thanks, this fix worked perfectly!
Denis June 12, 2014
Why apt upgrades mysql-common to version 5.6 when others mysql* packages have version 5.5? We use puppet to install mysql on our live servers and we have everything tested against mysql 5.5. Here is output from puppet agent Notice: /Stage[main]/Mysql55::Server/Package[mysql-common]/ensure: ensure changed ‘5.6.17-1dotdeb.1’ to ‘5.5.’ Notice: /Stage[main]/Mysql55::Server/Package[mysql-server]/ensure: ensure changed ‘5.5.37-0+wheezy1’ to ‘5.5.’ Notice: /Stage[main]/Mysql55::Server/Package[libmysqlclient18]/ensure: ensure changed ‘5.6.17-1dotdeb.1’ to ‘5.5.*’
- Guillaume Plessis June 12, 2014
  @Denis : you should put no version contraint on mysql-common, it’s a shared package between MySQL flavors/version : 5.5, 5.6, MariaDB
Basin June 13, 2014
Smooth upgrade on Wheezy from 5.6.17. Thanks Guillaume!
vmi June 16, 2014
Can someone please provide detailed steps to fix the following message when mysql starts up?
service mysql restart
[ ok ] Stopping MySQL database server: mysqld. [….] Starting MySQL database server: mysqldNo directory, logging in with HOME=/ . ok [info] Checking for tables which need an upgrade, are corrupt or were not closed cleanly..
mysql-server was installed on a clean install of wheezy using dotdeb repo.
Some, additional information in case it helps:
#uname -a Linux deblab 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3+deb7u2 x86_64 GNU/Linux
apt-get install mysql-server 2>&1 | tee std.txt
CONTENTS OF std.txt: http://www.hastebin.com/jijifagulu.avrasm
CONTENTS OF /var/log/mysql/error.log http://www.hastebin.com/mirizuwazu.vhdl
CONTENTS OF /etc/mysql/debian.cnf http://www.hastebin.com/ozekuhegan.hs
CONTENTS OF /etc/mysql/debian-start http://www.hastebin.com/kihoyadola.vala
CONTENTS OF /etc/mysql/my.cnf http://www.hastebin.com/xehivizije.vala
- Guillaume Plessis June 16, 2014
  @vmi : the “No directory, logging in with HOME=/” message is just a warning that I’ll try to get rid of in the next releases. You can ignore it safely.
  - vmi June 16, 2014
    Thank you for your response @Guillaume Also, is it safe to ignore the warning / error entries in error.log (Line numbers [82 -94])? http://www.hastebin.com/mirizuwazu.vhdl
    - Guillaume Plessis June 16, 2014
      @vmi : do you have any extra settings file in /etc/mysql/conf.d/?
      - vmi June 18, 2014
        So, any suggestions on how I can resolve the errors I’m receiving after a clean installation of mysql-server on a clean install of Wheezy?
        As I don’t have any custom config or prior install I’m assuming everyone must’ve come across this during installation.
    - Guillaume Plessis June 18, 2014
      @vmi : as said before, you can ignore the “No directory message”, and the check for “for tables which need an upgrade, are corrupt or were not closed cleanly” is normal. At the end, your MySQL server starts
      2014-06-15 18:00:51 6823 [Note] /usr/sbin/mysqld: ready for connections. Version: '5.6.19-1~dotdeb.1' socket: '/var/run/mysqld/mysqld.sock' port: 3306 (Debian)
      The installation is a success.
      About warnings in mysql/error.log, could you please run SHOW ENGINES and SHOW PLUGINS to ensure that InnoDB, Blackhole and Archive storage engines are up? About the limits, check this : /2014/04/02/mysql-5-6-17-for-wheezy/#comment-29419
      - vmi June 19, 2014
        Sorry for the delay in responding and thanks for your response.
        I added the following lines to /etc/security/limits.conf :
        soft nofile 32768
        hard nofile 65536 root soft nofile 32768 root hard nofile 65536
        And also ran SHOW ENGINES and SHOW PLUGINS as you requested, output in link below: http://www.hastebin.com/egogucopik.m
        However, I’m still seeing errors every time I restart mysql in /var/log/mysql/error.log Below are the contents of that file after erasing error.log and then service mysql restart. http://www.hastebin.com/zobarolutu.vhdl
        Mysql seems to be running but I’d like to have a clean error.log, so please let me know if I should just ignore the errors or if there is a way to set it right.
        Thanks again for your efforts w/ dotdeb project and still finding time to help newbs like me =)
        Guillaume Plessis June 19, 2014
        @vmi : everything is fine, you can ignore the warning message. Storage engines are loaded as expected. What is strange is that MySQL tries to load them a second time. That why I asked if you had extra config files, mentioning a plugin-load setting. But it’s ok.
vmi June 16, 2014
No, I haven’t added any extra config. mysql-server was installed on a clean installation of Debian Wheezy in a VM. With no pre existing version of mysql or any additional config. There is only one file present in /etc/mysql/conf.d: mysqld_safe_syslog.cnf (CONTENTS BELOW):
[mysqld_safe] syslog
Mike June 21, 2014
Clean new wheezy install, error while ‘apt-get install mysql-server’
It opens the GUI and asks fot a password…and then:
Starting MySQL database server: mysqldNo directory, logging in with HOME=/
. . . . . . . . . . . . . . failed! invoke-rc.d: initscript mysql, action “start” failed. dpkg: error processing mysql-server-5.6 (–configure): subprocess installed post-installation script returned error exit status 1 Errors were encountered while processing: mysql-server-5.6 E: Sub-process /usr/bin/dpkg returned an error code (1)
- Guillaume Plessis June 21, 2014
  @Mike : could you please take a look at your log files (/var/log/syslog, /var/log/mysql/error.log) for more details about what’s going wrong?
  - Mike June 21, 2014
    Did reinstall Debian 7, no more actions were applied except adding dotdeb to /etc/apt/sources.list.d/dotdeb.list
    After that ‘apt-get update && apt-get install mysql-server’ gives the same error.
    140621 16:20:05 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql 2014-06-21 16:20:06 7489 [Note] Plugin ‘FEDERATED’ is disabled. /usr/sbin/mysqld: Table ‘mysql.plugin’ doesn’t exist 2014-06-21 16:20:06 7489 [ERROR] Can’t open the mysql.plugin table. Please run mysql_upgrade to create it. 2014-06-21 16:20:06 7489 [Note] InnoDB: Using atomics to ref count buffer pool pages 2014-06-21 16:20:06 7489 [Note] InnoDB: The InnoDB memory heap is disabled 2014-06-21 16:20:06 7489 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins 2014-06-21 16:20:06 7489 [Note] InnoDB: Compressed tables use zlib 1.2.7 2014-06-21 16:20:06 7489 [Note] InnoDB: Using Linux native AIO 2014-06-21 16:20:06 7489 [Note] InnoDB: Using CPU crc32 instructions 2014-06-21 16:20:06 7f021a8cd720 InnoDB: Warning: io_setup() failed with EAGAIN. Will make 5 attempts before giving up. InnoDB: Warning: io_setup() attempt 1 failed. InnoDB: Warning: io_setup() attempt 2 failed. InnoDB: Warning: io_setup() attempt 3 failed. InnoDB: Warning: io_setup() attempt 4 failed. InnoDB: Warning: io_setup() attempt 5 failed. 2014-06-21 16:20:08 7f021a8cd720 InnoDB: Error: io_setup() failed with EAGAIN after 5 attempts. InnoDB: You can disable Linux Native AIO by setting innodb_use_native_aio = 0 in my.cnf 2014-06-21 16:20:08 7489 [ERROR] InnoDB: Fatal : Cannot initialize AIO sub-system 2014-06-21 16:20:08 7489 [ERROR] Plugin ‘InnoDB’ init function returned error. 2014-06-21 16:20:08 7489 [ERROR] Plugin ‘InnoDB’ registration as a STORAGE ENGINE failed. 2014-06-21 16:20:08 7489 [ERROR] Unknown/unsupported storage engine: InnoDB 2014-06-21 16:20:08 7489 [ERROR] Aborting
    - Mike June 21, 2014
      Tried another way: installed mysql 5.5 from official repos, then added dotdeb and upgraded. Upgrade process again failed, but the packages were updated. Manually ran ‘mysql_upgrade’ and now its working (although ‘service mysql …..’ is not working). BTW, you cant remove dotdeb mysql package if this error occurs :(
    - Guillaume Plessis June 21, 2014
      @Mike : the problem here is that your Linux kernel does not support native asynchronous IO. I suppose that you’re not using a stock Debian kernel (they support them by default). As written in your error logs, “You can disable Linux Native AIO by setting innodb_use_native_aio = 0 in my.cnf”. All should work fine then.
      - Mike June 22, 2014
        This problem is just because of another mysqld were running. After some another magical actions like install 5.5 - upgrade - then install mysql-server-5.6 (dont know why it was needed to install it again separately, but apt says that it was unresolved dependency) all works fine now. The problem is not in the core, it is for sure.
vmi June 21, 2014
@Guillaume I was able to solve the mystery behind the plugin errors I was receiving and decided to share the solution here in case other’s were wondering the same. To recap, the original errors in question showing up in /var/log/mysql/error.log were: 2014-06-19 01:12:07 3798 [ERROR] Function ‘innodb’ already exists 2014-06-19 01:12:07 3798 [Warning] Couldn’t load plugin named ‘innodb’ with soname ‘ha_innodb.so’. 2014-06-19 01:12:07 3798 [ERROR] Function ‘federated’ already exists 2014-06-19 01:12:07 3798 [Warning] Couldn’t load plugin named ‘federated’ with soname ‘ha_federated.so’. 2014-06-19 01:12:07 3798 [ERROR] Function ‘blackhole’ already exists 2014-06-19 01:12:07 3798 [Warning] Couldn’t load plugin named ‘blackhole’ with soname ‘ha_blackhole.so’. 2014-06-19 01:12:07 3798 [ERROR] Function ‘archive’ already exists 2014-06-19 01:12:07 3798 [Warning] Couldn’t load plugin named ‘archive’ with soname ‘ha_archive.so’.
Summary of solution: If a plugin is named both using a –plugin-load option and in the mysql.plugin table, the server starts but writes these messages to the error log: 100310 19:15:44 [ERROR] Function ‘plugin_name’ already exists 100310 19:15:44 [Warning] Couldn’t load plugin named ‘plugin_name’ with soname ‘plugin_object_file’.
I found the answer thanks to a post in the msyql forums: http://forums.mysql.com/read.php?22,614511,614601#msg-614601
Complete explaination here: http://dev.mysql.com/doc/refman/5.5/en/server-plugin-loading.html#server-plugin-installing
Personally, I solved this by removing all 4 offending rows in mysql.plugin by running the following: delete from mysql.plugin;
Afterwards, I was able to confirm that the plugin’s were still loading using SHOW PLUGINS; But this time no more error messages like above in error log.
Hope this helps and please let me know if there’s a better solution than what I’ve used.
– Thanks
- Guillaume Plessis June 21, 2014
  @vmi : Great! Thanks for this precious feedback. I’ll take a further look at these warnings when installing MySQL, and how the mysql.plugin table is populated.
iGuy June 22, 2014
Hi, After updating my debian 6 machine to debian 7, also updated MySQL 5.5 to 5.6 and now I’m noticing when I run dpkg –get-selections I have some 5.5 packages left over mysql-server-core-5.5 mysql-client-core-5.5 mysql-server-5.5 is this suppose to be this way because when I run apt-get remove mysql-server-5.5 I receive Package ‘mysql-server-5.5’ is not installed, so not removed
Thanks
- Guillaume Plessis June 22, 2014
  @iGuy : you can remove each of the ‘mysql-*-5.5’ packages safely.
Felipe June 25, 2014
I’m having this problem after a update:
Installing new version of config file /etc/mysql/debian-start … Installing new version of config file /etc/init.d/mysql … Installing new version of config file /etc/logrotate.d/mysql-server … [ ok ] Stopping MySQL database server: mysqld. [….] Starting MySQL database server: mysqldNo directory, logging in with HOME=/ [FAIL. . . . . . . . . . . . failed! invoke-rc.d: initscript mysql, action “start” failed. dpkg: error processing mysql-server-5.6 (–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-5.6; however: Package mysql-server-5.6 is not configured yet.
Using Wheezy..
Thanks!
- Guillaume Plessis June 25, 2014
  @Felipe : please check your log files (/var/log/syslog, /var/log/mysql*) to find what prevents MySQL from starting.
  - Felipe June 25, 2014
    Ive checked the logs but didnt find any tip (I’m too newbie). But I did something to fix it:
    apt-get remove –purge mysql-* (purge is what made the difference)
    apt-get install mysql-server
    Anyway, thanks for your work ,Guillaume (or Guilherme like we say in my country).
Cédric June 27, 2014
Bonjour,
L’erreur est toujours là de mon côté malgré le passage à MySQL 5.6.19 : est-ce que cette dernière version ne corrige pas le problème côté client ?
- Guillaume Plessis June 27, 2014
  Bonjour Cédric, de quelle erreur parles-tu exactement?
Paul July 2, 2014
I think there’s a conflict with percona packages. I use percona serwer and today when I tried to update my packages on debian wheezy I get error when I trie to update libperconaserver18.1. It prints that the mentioned package tries to overwrite libmysqlclient.so.18.1.0 which is in libmysqlclient18:amd64 5.6.19-1~dotdeb.1
- Paul July 3, 2014
  Percona team confirmed that this is bug (https://bugs.launchpad.net/percona-server/+bug/1336658) in their package.
Hendra July 10, 2014
@vmi : Thanks it worked ;)
- vmi July 10, 2014
  @Hendra: glad it worked out for you.b
huglester August 25, 2014
Hello,
I had trouble installing this on fresh setup. Error was: /var/lib/dpkg/info/mysql-server-5.6.postinst: line 111: logger: command not found /var/lib/dpkg/info/mysql-server-5.6.postinst: line 187: logger: command not found
The command which fixed it: apt-get install bsdutils –reinstall
Thanks and bye
pleaz August 29, 2014
hi, how i can delete this message: “No directory, logging in with HOME=/”. mysql work fine, logs haven’t warnings.
Robert September 16, 2014
In VMware WS 10 This warning pops up in the wordPress Debug Bar and in the logs: “Warning: mysqli_real_connect(): Headers and client library minor version mismatch. Headers:50538 Library:50619 in /usr/share/nginx/website02/wp-includes/wp-db.php on line 1379”
Any ideas how to rid off it?
TIA
- Guillaume Plessis September 16, 2014
  @Robert : /2014/04/04/about-the-mysql_connect-headers-and-client-library-minor-version-mismatch-warning-2/
Robert September 16, 2014
Hi Jerome, That was quick. I hope that you were not expecting me. :) Apologies I should have searched first. After reading the post you linked, I decide not to take any action after reading this: “The warning is thrown by libmysqlclient18 itself. And this is just a warning, there is no reason why any bad behavior would happen in that case.”
Thanks!

service mysql restart

apt-get install mysql-server 2>&1 | tee std.txt

No, I haven’t added any extra config. mysql-server was installed on a clean installation of Debian Wheezy in a VM. With no pre existing version of mysql or any additional config. There is only one file present in /etc/mysql/conf.d: mysqld_safe_syslog.cnf (CONTENTS BELOW):

[mysqld_safe] syslog

apt-get remove –purge mysql-* (purge is what made the difference)

apt-get install mysql-server