Default config contains deprecated directives

[Marcus Bointon]

When installing percona-server 5.6 on Ubuntu (5.6.21-70.1-698.trusty) I see these errors during installation and in the error logs:

2015-01-06 13:50:18 0 [Warning] Using unique option prefix key_buffer instead of key_buffer_size is deprecated and will be removed in a future release. Please use the full name instead.
2015-01-06 13:50:18 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).

The default my.cnf file contains these deprecated directives, but I cloned the percona-server repo and searched for these strings but couldn't find them, so I'm not sure where this config is coming from.

I also noticed that if these are overridden in a separate config file (in /etc/mysql/conf.d), these warnings are still shown, suggesting it's the config parser and not mysql itself that's complaining.

[Nilnandan Joshi (nilnandan-joshi)]

Unable to reproduce these warnings while install PS 5.6 on Ubuntu. so it doesn't seems that those files are coming with Percona packages. Can you please check all my.cnf files on your server with grep -r ? and see from where its taking old key_buffer_size variable settings?

Btw: is there any old version was installed on that server before you start installation of PS 5.6? it might be possible that old version is not completely purged so old my.cnf was there from where new installation was taking settings.

root@desktop:/var/lib# apt-get install Percona-Server-server-5.6
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
  libperconaserverclient18.1 percona-server-client-5.6 percona-server-common-5.6
Suggested packages:
  tinyca
The following NEW packages will be installed:
  libperconaserverclient18.1 percona-server-client-5.6 percona-server-common-5.6 percona-server-server-5.6
0 upgraded, 4 newly installed, 0 to remove and 54 not upgraded.
Need to get 0 B/14.0 MB of archives.
After this operation, 137 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Preconfiguring packages ...
Selecting previously unselected package percona-server-common-5.6.
(Reading database ... 230464 files and directories currently installed.)
Preparing to unpack .../percona-server-common-5.6_5.6.22-71.0-726.utopic_amd64.deb ...
Unpacking percona-server-common-5.6 (5.6.22-71.0-726.utopic) ...
Selecting previously unselected package libperconaserverclient18.1.
Preparing to unpack .../libperconaserverclient18.1_5.6.22-71.0-726.utopic_amd64.deb ...
Unpacking libperconaserverclient18.1 (5.6.22-71.0-726.utopic) ...
Selecting previously unselected package percona-server-client-5.6.
Preparing to unpack .../percona-server-client-5.6_5.6.22-71.0-726.utopic_amd64.deb ...
Unpacking percona-server-client-5.6 (5.6.22-71.0-726.utopic) ...
Processing triggers for man-db (2.7.0.2-2) ...
Setting up percona-server-common-5.6 (5.6.22-71.0-726.utopic) ...
Selecting previously unselected package percona-server-server-5.6.
(Reading database ... 230520 files and directories currently installed.)
Preparing to unpack .../percona-server-server-5.6_5.6.22-71.0-726.utopic_amd64.deb ...
Unpacking percona-server-server-5.6 (5.6.22-71.0-726.utopic) ...
Processing triggers for ureadahead (0.100.0-16) ...
Processing triggers for man-db (2.7.0.2-2) ...
Setting up libperconaserverclient18.1 (5.6.22-71.0-726.utopic) ...
Setting up percona-server-client-5.6 (5.6.22-71.0-726.utopic) ...
Setting up percona-server-server-5.6 (5.6.22-71.0-726.utopic) ...
 * Stopping MySQL (Percona Server) mysqld [ OK ]
2015-01-16 14:45:36 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2015-01-16 14:45:36 9576 [Note] Plugin 'FEDERATED' is disabled.
2015-01-16 14:45:36 9576 [Note] InnoDB: Using atomics to ref count buffer pool pages
2015-01-1...

[Marcus Bointon (marcus-synchromedia)]

This is on vagrant, so it's installing from scratch on a clean system that's never had MySQL on every time.

I can see one of those warnings in your example output.Ii think the correct my.cnf file is in packaging/deb-trusty/extra/my.cnf in this repo, but I can see that contains explicit_defaults_for_timestamp, which suggests that your installation is not coming from this repo, or is using some other my.cnf file.

Have I perhaps got the wrong repo?

[Hrvoje Matijakovic (hrvojem)]

@Nil,

Output should be visible in the error.log (for clean trusty install you can check /var/log/mysql/error.log). This is caused because PS-5.6 installs mysql-common package available in the distro repositories (currently mysql-common_5.5.40-0ubuntu0.14.04.1_all.deb).

root@trusty:~# aptitude why mysql-common
i percona-server-server-5.6 Depends libdbd-mysql-perl
i A libdbd-mysql-perl Depends libmysqlclient18 (>= 5.5.13-1)
i A libmysqlclient18 Depends mysql-common (>= 5.5.40-0ubuntu0.14.04.1)

[Marcus Bointon (marcus-synchromedia)]

I've attached a Vagrant config that reproduces this problem.

To run it, install vagrant, put the attached file into a folder, cd into it and run 'vagrant up'.

All it does is get an ubuntu trusty image, adds the percona repo and installs the percona-server-server package (5.6.22-71.0-726.trusty). The resulting installation has these bad directives in the /etc/my.cnf file.

I noticed during the installation that it installs mysql-common (5.5.40-0ubuntu0.14.04.1) as a dependency, which is probably where this is coming from.

I see that although percona-server-server-5.6 lists percona-server-common-5.6 as a dependency, percona-server-common-5.6 does not say it provides mysql-common - could that perhaps be the problem?

If I modify the vagrant file to explicitly install percona-server-common-5.6, the problem still occurs because mysql-common is still installed. Perhaps one of the sub-dependencies like libdbi-mysql-perl relies on it explicitly?

==> default: The following NEW packages will be installed:
==> default: libaio1 libdbd-mysql-perl libdbi-perl libmysqlclient18
==> default: libperconaserverclient18.1 mysql-common percona-server-client-5.6
==> default: percona-server-common-5.6 percona-server-server percona-server-server-5.6
==> default: 0 upgraded, 10 newly installed, 0 to remove and 30 not upgraded.
==> default: Need to get 15.8 MB of archives.
==> default: After this operation, 143 MB of additional disk space will be used.
==> default: Get:1 http://repo.percona.com/apt/ trusty/main percona-server-common-5.6 amd64 5.6.22-71.0-726.trusty [11.5 kB]
==> default: Get:2 http://archive.ubuntu.com/ubuntu/ trusty/main libaio1 amd64 0.3.109-4 [6,364 B]
==> default: Get:3 http://repo.percona.com/apt/ trusty/main libperconaserverclient18.1 amd64 5.6.22-71.0-726.trusty [566 kB]
==> default: Get:4 http://archive.ubuntu.com/ubuntu/ trusty-updates/main mysql-common all 5.5.40-0ubuntu0.14.04.1 [14.1 kB]
==> default: Get:5 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libmysqlclient18 amd64 5.5.40-0ubuntu0.14.04.1 [598 kB]
==> default: Get:6 http://repo.percona.com/apt/ trusty/main percona-server-client-5.6 amd64 5.6.22-71.0-726.trusty [1,392 kB]
==> default: Get:7 http://repo.percona.com/apt/ trusty/main percona-server-server-5.6 amd64 5.6.22-71.0-726.trusty [12.2 MB]
==> default: Get:8 http://archive.ubuntu.com/ubuntu/ trusty/main libdbi-perl amd64 1.630-1 [879 kB]
==> default: Get:9 http://archive.ubuntu.com/ubuntu/ trusty/main libdbd-mysql-perl amd64 4.025-1 [99.3 kB]
==> default: Get:10 http://repo.percona.com/apt/ trusty/main percona-server-server amd64 5.6.22-71.0-726.trusty [11.4 kB]
==> default: dpkg-preconfigure: unable to re-open stdin: No such file or directory
==> default: Fetched 15.8 MB in 19s (812 kB/s)
==> default: Selecting previously unselected package libaio1:amd64.
==> default: (Reading database ... 60964 files and directories currently installed.)
==> default: Preparing to unpack .../libaio1_0.3.109-4_amd64.deb ...
==> default: Unpacking libaio1:amd64 (0.3.109-4) ...
==> default: Selecting previously unselected package mysql-common.
==> default: Preparing to unpack .../mysql-common_5.5.40-0ubuntu0.14.04.1_all.deb ...
...

[Marcus Bointon (marcus-synchromedia)]

Sorry - I didn't see your comments as I was writing the above. Thanks for confirming the issue.

[Shahriyar Rzayev (rzayev-sehriyar)]

Percona now uses JIRA for bug reports so this bug report is migrated to: https://jira.percona.com/browse/PS-1598