12.04 Dist-upgrade breaks PHP extensions > pdo_mysql.so symbols

[aardvarkchris]

Bug Report: PHP Unable to load dynamic library pdo_mysql.so
[ Basic Information | Desired/Actual Behaviour | Steps to reproduce | More Info (incl. PHP Info) | System Information | Apport]

Hopefully I have included all relevant information here. Please let me know if you need more or if anything is unclear :)

Basic Information: Ubuntu 12.04 LTS x64, Apache 2.2.22 (Built Feb 13 2012), PHP 5.4.1 (although DPKG states installed packages are php5_5.3.10), php5-mysql (*not* php5-mysqlnd)

Desired Behaviour:
Launch PHP with PDO mysql_driver error free, enabled and working.

Actual Behaviour:
PHP launches with error in logfile:
 PHP Warning: PHP Startup: Unable to load dynamic library '/usr/lib/php5/20090626/pdo_mysql.so' - /usr/lib/php5/20090626/pdo_mysql.so: undefined symbol: pdo_parse_params in Unknown on line 0

Steps to Reproduce:
Install Ubuntu 12.04 LTS

Successfully install php5, php-mysql using apt-get (no errors or warnings):
sudo apt-get install php5
sudo apt-get install php5-mysql

Install Symfony and Streeme with instructions on Google Code (basically svn co http://streeme.url)

Perform package & distribution upgrade:
apt-get dist-upgrade

Start PHP:
service apache2 restart

Receive warning in error log:
 PHP Warning: PHP Startup: Unable to load dynamic library '/usr/lib/php5/20090626/pdo_mysql.so' - /usr/lib/php5/20090626/pdo_mysql.so: undefined symbol: pdo_parse_params in Unknown on line 0

[Further steps to reproduce]

Attempt to rescan music (./symfony scan-media --type=filesystem)

Receive warning:
Couldn't locate driver named mysql

More Info:
[ Description | PHP Info | Related Files ]
I have recently upgraded (via sudo apt-get dist-upgrade) my system to 12.04 Ubuntu x64.

Previously I had a very nice app called Streeme, which I used to listen to my music anywhere. It uses a framework called Symfony (Streeme requires Symfony <=1.4), and hooks into a mySQL database where it stores all of it's 'stuff' (library info, paths, users, etc).

I have a working PHP5 and mySQL setup on the machine. This is verified by the use of eGroupware and phpMyAdmin (plus PHP scripts which will happily talk to the mySQL database using mysql_connect()). Four weeks ago the Apache2 webserver apache2 was replaced in place with the apache2-mtm-itk package to allow the webserver to function with different UIDs. This was reversed two weeks ago, but the problem still exists. Before, during and after there was no issue with mySQL access through phpMyAdmin or eGroupware, or a PHP script.

Attempting to revive Streeme after the upgrade (not everything works directly after an upgrade and from experience a new Streeme installation is preferable to stitching an old one together, although I don't know why- plus the hard drive with all the music on it got a kicking from which it could not recover, so I might as well start again!) has totally failed with the error:

Couldn't locate driver named mysql

Obviously this is a symfony framework error. However, I know that mysql should be available. After some investigation, it turns out Symfony uses PDO (particularly pdo_mysql) to access the database (and, in turn, during a media scan or doctrine installation (think bootstrapping) PHP directs Symfony). Further investigation directed me to check that the pdo was enabled correctly, so please see the following from php_info():

Loaded Configuration File /etc/php5/apache2/php.ini

.ini files parsed: ... /etc/php5/apache2/conf.d/pdo_mysql.ini ...

PHP API 20090626
PHP Extension 20090626
extension_dir /usr/lib/php5/20090626

mysql
MySQL Support enabled
Active Persistent Links 0
Active Links 0
Client API version 5.5.24
MYSQL_MODULE_TYPE external
MYSQL_SOCKET /var/run/mysqld/mysqld.sock
MYSQL_INCLUDE -I/usr/include/mysql
MYSQL_LIBS -L/usr/lib/x86_64-linux-gnu -lmysqlclient_r

mysql.allow_local_infile On On
mysql.allow_persistent On On
mysql.connect_timeout 60 60
mysql.default_host no value no value
mysql.default_password no value no value
mysql.default_port no value no value
mysql.default_socket /var/run/mysqld/mysqld.sock /var/run/mysqld/mysqld.sock
mysql.default_user no value no value
mysql.max_links Unlimited Unlimited
mysql.max_persistent Unlimited Unlimited
mysql.trace_mode Off Off

PDO
PDO support enabled
PDO drivers mysql, sqlite

So PDO is, theoretically, enabled. There is a similar output when using the CLI configuration file (/etc/php5/cli/php.ini)

However there is an error appearing in the PHP error log:

PHP Warning: PHP Startup: Unable to load dynamic library '/usr/lib/php5/20090626/pdo_mysql.so' - /usr/lib/php5/20090626/pdo_mysql.so: undefined symbol: pdo_parse_params in Unknown on line 0

Which seems to indicate that there is no file there (which is not true):
-rw-r--r-- 1 root root 31056 Jun 13 18:36 /usr/lib/php5/20090626/pdo_mysql.so
(In fact, all PDO related symbols have a timestamp of June 13, 18:36)

I have checked in all /etc/php5/*/ folders for conf.d/pdo.ini, mysql.ini, pdo_mysql.ini and they all exist and have the correct directives:
[e.g:]
; configuration for php PDO module
extension=pdo.so

But if I ask for the extension_dir using: php -c /etc/php2/apache2/php.ini -i |grep extension_dir
extension_dir => /usr/local/lib/php/extensions/no-debug-zts-20100525 => /usr/local/lib/php/extensions/no-debug-zts-20100525

This directory (/usr/local/lib/php/extensions/no-debug-zts-20100525) does not exist, but PHP does not seem to look for it or use it anyway (nothing in the error log or php_info() mentions this folder). It is not even mentioned in any of the common configuration files, so I have *no idea* where PHP gets this information.

So it seems that somewhere, most likely in some upgrade, this file was altered and refuses to load, causing symfony, and other packages which depend on the mysql PDO driver, to fail.

I have tried to dpkg-reconfigure the various packages mentioned below but it does not fix the problem. Everything else to do with PHP works. I can only see that this is a bug with PHP which is causing symfony to fail to find the correct drivers it requires. This has worked previously on this machine.

Further Information:
[ PHP Version | Debsums | PHP Package versions | OS Information | ldd Output ]

Output of php -c /etc/php5/apache2 --version
PHP 5.4.1 (cli) (built: Apr 29 2012 18:27:47)
Copyright (c) 1997-2012 The PHP Group
Zend Engine v2.4.0, Copyright (c) 1998-2012 Zend Technologies

Debsums info:
debsums -e php5-common
/etc/php5/conf.d/pdo.ini OK
/etc/cron.d/php5 OK

 debsums -e libapache2-mod-php5
/etc/apache2/mods-available/php5.load OK
/etc/apache2/mods-available/php5.conf OK

debsums -e php5-mysql
/etc/php5/conf.d/mysqli.ini OK
/etc/php5/conf.d/mysql.ini OK
/etc/php5/conf.d/pdo_mysql.ini OK

PHP Installed Packages (despite php --version stating PHP version is 5.4.1)
php5_5.3.10-1ubuntu3.2_all.deb
php5-cli_5.3.10-1ubuntu3.2_amd64.deb
php5-common_5.3.10-1ubuntu3.2_amd64.deb
php5-curl_5.3.10-1ubuntu3.2_amd64.deb
php5-dev_5.3.10-1ubuntu3.2_amd64.deb
php5-gd_5.3.10-1ubuntu3.2_amd64.deb
php5-ldap_5.3.10-1ubuntu3.2_amd64.deb
php5-mysql_5.3.10-1ubuntu3.2_amd64.deb
php5-sqlite_5.3.10-1ubuntu3.2_amd64.deb
php-db_1.7.13-2_all.deb
php-geshi_1.0.8.4-1_all.deb
php-http_1.4.1-1_all.deb
php-pear_5.3.10-1ubuntu3.2_all.deb

apt-cache policy php5
php5:
  Installed: 5.3.10-1ubuntu3.2
  Candidate: 5.3.10-1ubuntu3.2
  Version table:
 *** 5.3.10-1ubuntu3.2 0
        500 http://gb.archive.ubuntu.com/ubuntu/ precise-updates/main amd64 Packages
        500 http://security.ubuntu.com/ubuntu/ precise-security/main amd64 Packages
        100 /var/lib/dpkg/status
     5.3.10-1ubuntu3 0
        500 http://gb.archive.ubuntu.com/ubuntu/ precise/main amd64 Packages

 apt-cache policy php5-mysql
php5-mysql:
  Installed: 5.3.10-1ubuntu3.2
  Candidate: 5.3.10-1ubuntu3.2
  Version table:
 *** 5.3.10-1ubuntu3.2 0
        500 http://gb.archive.ubuntu.com/ubuntu/ precise-updates/main amd64 Packages
        500 http://security.ubuntu.com/ubuntu/ precise-security/main amd64 Packages
        100 /var/lib/dpkg/status
     5.3.10-1ubuntu3 0
        500 http://gb.archive.ubuntu.com/ubuntu/ precise/main amd64 Packages

php5-common:
  Installed: 5.3.10-1ubuntu3.2
  Candidate: 5.3.10-1ubuntu3.2
  Version table:
 *** 5.3.10-1ubuntu3.2 0
        500 http://gb.archive.ubuntu.com/ubuntu/ precise-updates/main amd64 Packages
        500 http://security.ubuntu.com/ubuntu/ precise-security/main amd64 Packages
        100 /var/lib/dpkg/status
     5.3.10-1ubuntu3 0
        500 http://gb.archive.ubuntu.com/ubuntu/ precise/main amd64 Packages

Release Information: lsb_release -rd
Description: Ubuntu 12.04 LTS
Release: 12.04

OS Information: uname -a
Linux [snip] 3.2.0-25-generic #40-Ubuntu SMP Wed May 23 20:30:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

ldd /usr/lib/php5/20090626/pdo_mysql.so
        linux-vdso.so.1 => (0x00007fff05fe1000)
        libmysqlclient.so.18 => /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18 (0x00007f85b1123000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f85b0d66000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f85b0b4e000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f85b094a000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f85b072d000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f85b0432000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f85b188a000)

Apport:
Unfortunately apport has not registered a crash.
apport-cli -p php5 --save ~/php5.bug
No pending crash reports. Try --help for more information.

apport-cli -p php5-mysql --save ~/php5mysql.bug
No pending crash reports. Try --help for more information.

[Clint Byrum (clint-fewbar)]

Hi, and thank you for taking the time to file such a detailed bug report!

"PHP Installed Packages (despite php --version stating PHP version is 5.4.1)"

Your cli PHP version is different than the libapache2-mod-php5 version. I suspect you have installed a version of php in /usr/local/bin that is not from the repositories.

Since the setup instructions have you running commands with the PHP CLI, this is likely to cause problems, if not confusion.

I ran through the entire install of streeme (cool app!) and it works flawlessly with a clean brand new installed precise system.

Unless there is some step I've missed, I don't think this is an issue we can solve in Ubuntu. Please feel free to set the bug back to 'New' if you disagree, or open a new bug with 'ubuntu-bug php5'.

[aardvarkchris (chris-adam-smith)]

@clint

Thanks- you're quite right! I don't know why I would have done that, now to find out what's broken with the 'downgrade' of PHP.

Know anything popular that would have required building PHP 5.4 from source? Guess I'll have to keep an eye on the logs, lame!

Moved the /usr/local/bin/php to /usr/local/bin/php.old.

Now $ which php
gives /usr/bin/php

But running $ php
gives: /usr/local/bin/php - not found

So I symlinked /usr/local/bin/php to /usr/bin/php and off we go :)

Thanks again.

[Shane Hollis (k-shane)]

for what it's worth. I ran into a similar problem.
The pdo.ini file was missing but had a pdo_mysql.ini file.
Added a pdo.ini file, pointed it at pdo.so and everything worked.

/etc/php5/cli/conf.d# cat pdo.ini
; configuration for php MySQL module
extension=pdo.so