Unable to upgrade PHP with Atomic Repo

[KrazyBob]

I trhink I am making things worse by trying, but other Virtuozzo nodes allowed the same upgrade.

This began as an attempt to upgrade zend. But it resulted in errors as well.

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-bash-3.2# php -v
Failed loading /usr/lib64/php/modules//php_ioncube_loader_lin_5.1_x86_64.so:  /usr/lib64/php/modules//php_ioncube_loader_lin_5.1_x86_64.so: undefined symbol: zend_unmangle_property_name_ex
PHP 5.2.12 (cli) (built: Jan 31 2010 12:53:32) 
Copyright (c) 1997-2009 The PHP Group
Zend Engine v2.2.0, Copyright (c) 1998-2009 Zend Technologies
    with Zend Optimizer v3.3.9, Copyright (c) 1998-2009, by Zend Technologies

So I tried to upgrade PHP. Honestly, I am an intermnediate admin and don't know how to move forward to correct the errors.

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--> Running transaction check
--> Processing Dependency: php-cli = 5.1.6-23.2.el5_3 for package: php
--> Processing Dependency: php-common = 5.1.6-23.2.el5_3 for package: php
---> Package php.x86_64 0:5.2.12-3.el5.art set to be updated
--> Finished Dependency Resolution
php-5.1.6-23.2.el5_3.x86_64 from installed has depsolving problems
  --> Missing Dependency: php-common = 5.1.6-23.2.el5_3 is needed by package php-5.1.6-23.2.el5_3.x86_64 (installed)
php-5.1.6-23.2.el5_3.x86_64 from installed has depsolving problems
  --> Missing Dependency: php-cli = 5.1.6-23.2.el5_3 is needed by package php-5.1.6-23.2.el5_3.x86_64 (installed)
--> Running transaction check
--> Processing Dependency: php-cli = 5.1.6-23.2.el5_3 for package: php
--> Processing Dependency: php-common = 5.1.6-23.2.el5_3 for package: php
--> Finished Dependency Resolution
php-5.1.6-23.2.el5_3.x86_64 from installed has depsolving problems
  --> Missing Dependency: php-common = 5.1.6-23.2.el5_3 is needed by package php-5.1.6-23.2.el5_3.x86_64 (installed)
php-5.1.6-23.2.el5_3.x86_64 from installed has depsolving problems
  --> Missing Dependency: php-cli = 5.1.6-23.2.el5_3 is needed by package php-5.1.6-23.2.el5_3.x86_64 (installed)
--> Running transaction check
---> Package libXaw.x86_64 0:1.0.2-8.1 set to be updated
---> Package libXmu.x86_64 0:1.0.2-5 set to be updated
---> Package libXt.x86_64 0:1.0.2-3.1.fc6 set to be updated
--> Processing Dependency: php-cli = 5.1.6-23.2.el5_3 for package: php
---> Package php-cli.x86_64 0:5.2.12-3.el5.art set to be updated
--> Processing Dependency: php-common = 5.1.6-23.2.el5_3 for package: php
---> Package php-common.x86_64 0:5.2.12-3.el5.art set to be updated
---> Package php-gd.x86_64 0:5.2.12-3.el5.art set to be updated
---> Package php-imap.x86_64 0:5.2.12-3.el5.art set to be updated
---> Package php-mbstring.x86_64 0:5.2.12-3.el5.art set to be updated
---> Package php-mysql.x86_64 0:5.2.12-3.el5.art set to be updated
---> Package php-pdo.x86_64 0:5.2.12-3.el5.art set to be updated
---> Package php-xml.x86_64 0:5.2.12-3.el5.art set to be updated
---> Package t1lib.x86_64 0:5.1.2-2.el5.art set to be updated
--> Finished Dependency Resolution
php-5.1.6-23.2.el5_3.x86_64 from installed has depsolving problems
  --> Missing Dependency: php-common = 5.1.6-23.2.el5_3 is needed by package php-5.1.6-23.2.el5_3.x86_64 (installed)
php-5.1.6-23.2.el5_3.x86_64 from installed has depsolving problems
  --> Missing Dependency: php-cli = 5.1.6-23.2.el5_3 is needed by package php-5.1.6-23.2.el5_3.x86_64 (installed)
--> Running transaction check
---> Package libXaw.x86_64 0:1.0.2-8.1 set to be updated
---> Package libXmu.x86_64 0:1.0.2-5 set to be updated
---> Package libXt.x86_64 0:1.0.2-3.1.fc6 set to be updated
---> Package php-gd.x86_64 0:5.2.12-3.el5.art set to be updated
--> Processing Dependency: php-common = 5.2.12-3.el5.art for package: php-gd
---> Package php-imap.x86_64 0:5.2.12-3.el5.art set to be updated
--> Processing Dependency: php-common = 5.2.12-3.el5.art for package: php-imap
---> Package php-mbstring.x86_64 0:5.2.12-3.el5.art set to be updated
--> Processing Dependency: php-common = 5.2.12-3.el5.art for package: php-mbstring
---> Package php-mysql.x86_64 0:5.2.12-3.el5.art set to be updated
--> Processing Dependency: php-common = 5.2.12-3.el5.art for package: php-mysql
---> Package php-pdo.x86_64 0:5.2.12-3.el5.art set to be updated
--> Processing Dependency: php-common = 5.2.12-3.el5.art for package: php-pdo
---> Package php-xml.x86_64 0:5.2.12-3.el5.art set to be updated
--> Processing Dependency: php-common = 5.2.12-3.el5.art for package: php-xml
---> Package t1lib.x86_64 0:5.1.2-2.el5.art set to be updated
--> Finished Dependency Resolution
php-imap-5.2.12-3.el5.art.x86_64 from atomic has depsolving problems
  --> Missing Dependency: php-common = 5.2.12-3.el5.art is needed by package php-imap-5.2.12-3.el5.art.x86_64 (atomic)
php-mbstring-5.2.12-3.el5.art.x86_64 from atomic has depsolving problems
  --> Missing Dependency: php-common = 5.2.12-3.el5.art is needed by package php-mbstring-5.2.12-3.el5.art.x86_64 (atomic)
php-mysql-5.2.12-3.el5.art.x86_64 from atomic has depsolving problems
  --> Missing Dependency: php-common = 5.2.12-3.el5.art is needed by package php-mysql-5.2.12-3.el5.art.x86_64 (atomic)
php-gd-5.2.12-3.el5.art.x86_64 from atomic has depsolving problems
  --> Missing Dependency: php-common = 5.2.12-3.el5.art is needed by package php-gd-5.2.12-3.el5.art.x86_64 (atomic)
php-pdo-5.2.12-3.el5.art.x86_64 from atomic has depsolving problems
  --> Missing Dependency: php-common = 5.2.12-3.el5.art is needed by package php-pdo-5.2.12-3.el5.art.x86_64 (atomic)
php-xml-5.2.12-3.el5.art.x86_64 from atomic has depsolving problems
  --> Missing Dependency: php-common = 5.2.12-3.el5.art is needed by package php-xml-5.2.12-3.el5.art.x86_64 (atomic)

Packages skipped because of dependency problems:
    libXaw-1.0.2-8.1.x86_64 from base
    libXmu-1.0.2-5.x86_64 from base
    libXt-1.0.2-3.1.fc6.x86_64 from base
    php-5.2.12-3.el5.art.x86_64 from atomic
    php-cli-5.2.12-3.el5.art.x86_64 from atomic
    php-common-5.2.12-3.el5.art.x86_64 from atomic
    php-gd-5.2.12-3.el5.art.x86_64 from atomic
    php-imap-5.2.12-3.el5.art.x86_64 from atomic
    php-mbstring-5.2.12-3.el5.art.x86_64 from atomic
    php-mysql-5.2.12-3.el5.art.x86_64 from atomic
    php-pdo-5.2.12-3.el5.art.x86_64 from atomic
    php-xml-5.2.12-3.el5.art.x86_64 from atomic
    t1lib-5.1.2-2.el5.art.x86_64 from atomic

[scott]

That looks like you've got a customized distro there. Perhaps someone has excluded packages in your yum configs, which is what is causing you problems. Try running:

yum --disableexcludes=all upgrade

[KrazyBob]

This is a new server with Plesk 9.3 installed by their installer. Other servers that we installed at the same time didn't have a problem. In this case it looks like PHP 5.2.x won't install, causing errors down the line. I don't know how to force PHP 5.2.x to install.

I dealt with the ioncube-loader issue by first using yum to remove the Plesk installed version, using yum to install the atomic version, and then used the Plesk installer to reinstall PPWSE, which was removed when ioncube was removed.

I am still left with the inability to update PHP.

[scott]

See this:

-bash-3.2# php -v

thats not normal, this tells me you're not running the default image. And if the prompts are different, then what else is on the system?

[KrazyBob]

Huh??? That's the standard command to ask what version of php is running. Plese recall that we are running Virtuozzo and then Plesk inside of it. So that is the prompt. The prompt above the container is:

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Last login: Tue Feb 23 13:20:54 2010 from monitor
[root@hw003 ~]#

But the operation is still the same.

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[root@hw003 ~]# vzctl enter 107
entered into VE 107
-bash-3.2 clss01 # php -v
Failed loading /usr/lib64/php/modules//php_ioncube_loader_lin_5.1_x86_64.so:  /usr/lib64/php/modules//php_ioncube_loader_lin_5.1_x86_64.so: undefined symbol: zend_unmangle_property_name_ex
PHP 5.2.12 (cli) (built: Jan 31 2010 12:53:32) 
Copyright (c) 1997-2009 The PHP Group
Zend Engine v2.2.0, Copyright (c) 1998-2009 Zend Technologies
    with Zend Optimizer v3.3.9, Copyright (c) 1998-2009, by Zend Technologies
-bash-3.2 clss01 # 

As I mentioned, the solution for this was found by first removing php-ioncube-loader, which also removes Plesk's PPWS, use yum to install the newer version of php-ioncube-loader, and then use the Plesk interactive installer to reinstall PPWSE.

What has not been corrected is one server that refuses to allow me to upgrade PHP. It stays at 5.1.6 and errors when attempting to use yum to update it.

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-bash-3.2 clss03 # php -v
PHP 5.1.6 (cli) (built: Apr  7 2009 08:00:18) 
Copyright (c) 1997-2006 The PHP Group
Zend Engine v2.1.0, Copyright (c) 1998-2006 Zend Technologies
    with the ionCube PHP Loader v3.1.28, Copyright (c) 2002-2007, by ionCube Ltd.
-bash-3.2 clss03 # yum update php
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * addons: mirror.san.fastserv.com
 * atomic: www.atomicorp.com
 * base: mirrors.netdna.com
 * epel: mirror.hmc.edu
 * extras: mirror.hmc.edu
 * updates: mirror.san.fastserv.com
addons                                                                       |  951 B     00:00     
atomic                                                                       | 1.9 kB     00:00     
base                                                                         | 2.1 kB     00:00     
epel                                                                         | 3.4 kB     00:00     
extras                                                                       | 1.1 kB     00:00     
updates                                                                      | 1.9 kB     00:00     
updates/primary_db                                                           | 636 kB     00:00     
Setting up Update Process
Resolving Dependencies
--> Running transaction check
--> Processing Dependency: php <= 5.2.0 for package: php-sqlite2
---> Package php.x86_64 0:5.2.12-3.el5.art set to be updated
--> Processing Dependency: php-common = 5.2.12-3.el5.art for package: php
--> Processing Dependency: php-cli = 5.2.12-3.el5.art for package: php
--> Running transaction check
--> Processing Dependency: php <= 5.2.0 for package: php-sqlite2
---> Package php-cli.x86_64 0:5.2.12-3.el5.art set to be updated
--> Processing Dependency: php-common = 5.1.6-23.2.el5_3 for package: php-pdo
--> Processing Dependency: php-common = 5.1.6-23.2.el5_3 for package: php-mbstring
--> Processing Dependency: php-common = 5.1.6-23.2.el5_3 for package: php-xml
--> Processing Dependency: php-common = 5.1.6-23.2.el5_3 for package: php-mysql
--> Processing Dependency: php-common = 5.1.6-23.2.el5_3 for package: php-gd
--> Processing Dependency: php-common = 5.1.6-23.2.el5_3 for package: php-imap
---> Package php-common.x86_64 0:5.2.12-3.el5.art set to be updated
--> Running transaction check
--> Processing Dependency: php <= 5.2.0 for package: php-sqlite2
---> Package php-gd.x86_64 0:5.2.12-3.el5.art set to be updated
--> Processing Dependency: libt1.so.5()(64bit) for package: php-gd
---> Package php-imap.x86_64 0:5.2.12-3.el5.art set to be updated
---> Package php-mbstring.x86_64 0:5.2.12-3.el5.art set to be updated
---> Package php-mysql.x86_64 0:5.2.12-3.el5.art set to be updated
---> Package php-pdo.x86_64 0:5.2.12-3.el5.art set to be updated
---> Package php-xml.x86_64 0:5.2.12-3.el5.art set to be updated
--> Running transaction check
--> Processing Dependency: php <= 5.2.0 for package: php-sqlite2
---> Package t1lib.x86_64 0:5.1.2-2.el5.art set to be updated
--> Processing Dependency: libXaw.so.7()(64bit) for package: t1lib
--> Processing Dependency: libXt.so.6()(64bit) for package: t1lib
--> Running transaction check
---> Package libXaw.x86_64 0:1.0.2-8.1 set to be updated
--> Processing Dependency: libXmu.so.6()(64bit) for package: libXaw
---> Package libXt.x86_64 0:1.0.2-3.1.fc6 set to be updated
--> Processing Dependency: php <= 5.2.0 for package: php-sqlite2
--> Running transaction check
---> Package libXmu.x86_64 0:1.0.2-5 set to be updated
--> Processing Dependency: php <= 5.2.0 for package: php-sqlite2
--> Finished Dependency Resolution
php-sqlite2-5.1.6-200705230937.x86_64 from installed has depsolving problems
  --> Missing Dependency: php <= 5.2.0 is needed by package php-sqlite2-5.1.6-200705230937.x86_64 (installed)
Error: Missing Dependency: php <= 5.2.0 is needed by package php-sqlite2-5.1.6-200705230937.x86_64 (installed)
 You could try using --skip-broken to work around the problem
 You could try running: package-cleanup --problems
                        package-cleanup --dupes
                        rpm -Va --nofiles --nodigest
-bash-3.2 clss03 #

[mikeshinn]

The prompt itself looks strange:

-bash-3.2 clss01 #

[faris]

The prompt itself looks strange:

-bash-3.2 clss01 #

It is actually normal for Virtuozzo, sort of (if you ignore the clss01 but that may be the hostname and therefor normal for his particular installation) .

Basically, with Virtuozzo, when you "enter" a container from the hardware node (as opposed to sshing in directly to it), you get the above kind of bash prompt, with version.

HOWEVER, if you then "su -", which I do habitually for just this very reason, you get a "normal" prompt, and obviously you are plonked in the /root directory.

The process goes something like this:
Login to hardware node via ssh
vzctl enter <container id>
Prompt: -bash-<ver>#
su -
Prompt: [user@hostname ~]#

[KrazyBob]

Because we have so many containers we append the hostname with PS. But you are absolutely correct -- this is a normal prompt for entering a Virtuzzo container from the hardware node. If one enters the container directly using ssh one gets the full prompt. The prompt, of course, has nothing to do with the original issue of being unable to upgrade PHP on this server.

[scott]

Well its definitely not a repo problem, you've got a custom environment there. Thats the issue

[KrazyBob]

There is nothing custom here. A Virtuozzo container is no different than a dedicated server. It installs the same OS into dedicated space. As I've mentioned several times I have used the Atomic repo and updated PHP on numerous other installations. Just this ONE won't update. Virtuozzo by Parallels (Plesk/SW-Soft) is as industry standard as it gets Please understand that no one is blaming Atomic -- we're simply saying that an error has occurred and are looking for a solution.

[faris]

Anyway, this all resolves around php-sqlite2 - isn't this the file that's been mentioned in php update failures an awful lot of times here and on the Parallels forum?

KrazyBob -- try a yum clean all just in case? I know it is a fresh install, but...

Alternatively try to remove it, unless there are particularly bad dependancies?

Faris.

[KrazyBob]

This server is online with customers. Will yum clean cause any harm?

[faris]

Not that I'm aware of. It just removes yum's caches and metadata and makes it re-generate them. It also deleted old rpms (the actual rpms, not the files they put in place).

Don't do it until someone else confirms though. I'm not taking the responsibility

Faris.