Error on dependencies

[genarg]

This is the log I am getting over Webmin. I allways used atomicorp repo. How can it be fixed.

Code: Select all

Now updating mysql ..

    Installing package(s) with command yum -y install mysql ..

    Loaded plugins: fastestmirror
    Existing lock /var/run/yum.pid: another copy is running as pid 31418.
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  53 M RSS (243 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:09 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  54 M RSS (244 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:11 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  54 M RSS (245 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:13 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  55 M RSS (246 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:15 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  56 M RSS (247 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:17 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  57 M RSS (248 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:19 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  58 M RSS (249 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:21 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  59 M RSS (250 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:23 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  60 M RSS (251 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:25 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  61 M RSS (252 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:27 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  62 M RSS (252 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:29 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  62 M RSS (253 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:31 ago
        State  : Running, pid: 31418
    Another app is currently holding the yum lock; waiting for it to exit...
      The other application is: yum
        Memory :  63 M RSS (254 MB VSZ)
        Started: Tue Oct 18 09:22:53 2011 - 00:33 ago
        State  : Running, pid: 31418
    Loading mirror speeds from cached hostfile
     * Webmin: download.webmin.com
     * atomic: www2.atomicorp.com
     * base: linux.mirrors.es.net
     * extras: mirrors.usc.edu
     * updates: mirrors.usc.edu
    Setting up Install Process
    Resolving Dependencies
    --> Running transaction check
    --> Processing Dependency: mysql = 5.1.59-1.el5.art for package: mysql-libs
    --> Processing Dependency: mysql = 5.1.59-1.el5.art for package: mysql-libs
    --> Processing Dependency: mysql = 5.1.59-1.el5.art for package: mysql-server
    ---> Package mysql.i386 0:5.5.16-1.el5.art set to be updated
    ---> Package mysql.x86_64 0:5.5.16-1.el5.art set to be updated
    --> Running transaction check
    --> Processing Dependency: libmysqlclient.so.16 for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16()(64bit) for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: php-mysql
    ---> Package mysql-libs.i386 0:5.5.16-1.el5.art set to be updated
    ---> Package mysql-libs.x86_64 0:5.5.16-1.el5.art set to be updated
    ---> Package mysql-server.x86_64 0:5.5.16-1.el5.art set to be updated
    --> Processing Dependency: libaio.so.1(LIBAIO_0.4)(64bit) for package: mysql-server
    --> Processing Dependency: libaio.so.1(LIBAIO_0.1)(64bit) for package: mysql-server
    --> Processing Dependency: libaio.so.1()(64bit) for package: mysql-server
    --> Running transaction check
    ---> Package libaio.x86_64 0:0.3.106-5 set to be updated
    --> Processing Dependency: libmysqlclient.so.16 for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: php-mysql
    ---> Package mysqlclient16.x86_64 0:5.1.57-1.el5.art set to be updated
    --> Finished Dependency Resolution
    php-mysql-5.3.8-1.el5.art.i386 from installed has depsolving problems
      --> Missing Dependency: libmysqlclient.so.16 is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
    php-mysql-5.3.8-1.el5.art.i386 from installed has depsolving problems
      --> Missing Dependency: libmysqlclient.so.16(libmysqlclient_16) is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
    Error: Missing Dependency: libmysqlclient.so.16(libmysqlclient_16) is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
    Error: Missing Dependency: libmysqlclient.so.16 is needed by package php-mysql-5.3.8-1.el5.art.i386 (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
    The program package-cleanup is found in the yum-utils package.

    .. install failed!


Now updating mysql-libs ..

    Installing package(s) with command yum -y install mysql-libs ..

    Loaded plugins: fastestmirror
    Loading mirror speeds from cached hostfile
     * Webmin: download.webmin.com
     * atomic: www2.atomicorp.com
     * base: linux.mirrors.es.net
     * extras: mirrors.usc.edu
     * updates: mirrors.usc.edu
    Setting up Install Process
    Resolving Dependencies
    --> Running transaction check
    --> Processing Dependency: libmysqlclient.so.16 for package: mysql
    --> Processing Dependency: libmysqlclient.so.16 for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: mysql
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: php-mysql
    --> Processing Dependency: libmysqlclient_r.so.16 for package: mysql
    --> Processing Dependency: libmysqlclient_r.so.16(libmysqlclient_16) for package: mysql
    --> Processing Dependency: mysql-libs = 5.1.59-1.el5.art for package: mysql
    --> Processing Dependency: mysql-libs = 5.1.59-1.el5.art for package: mysql
    --> Processing Dependency: libmysqlclient.so.16()(64bit) for package: mysql-server
    --> Processing Dependency: libmysqlclient.so.16()(64bit) for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: mysql-server
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: php-mysql
    --> Processing Dependency: libmysqlclient_r.so.16()(64bit) for package: mysql-server
    --> Processing Dependency: libmysqlclient_r.so.16(libmysqlclient_16)(64bit) for package: mysql-server
    ---> Package mysql-libs.i386 0:5.5.16-1.el5.art set to be updated
    ---> Package mysql-libs.x86_64 0:5.5.16-1.el5.art set to be updated
    --> Running transaction check
    ---> Package mysql.i386 0:5.5.16-1.el5.art set to be updated
    ---> Package mysql.x86_64 0:5.5.16-1.el5.art set to be updated
    --> Processing Dependency: libmysqlclient.so.16 for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: php-mysql
    ---> Package mysql-server.x86_64 0:5.5.16-1.el5.art set to be updated
    --> Processing Dependency: libaio.so.1(LIBAIO_0.4)(64bit) for package: mysql-server
    --> Processing Dependency: libaio.so.1(LIBAIO_0.1)(64bit) for package: mysql-server
    --> Processing Dependency: libaio.so.1()(64bit) for package: mysql-server
    ---> Package mysqlclient16.x86_64 0:5.1.57-1.el5.art set to be updated
    --> Running transaction check
    ---> Package libaio.x86_64 0:0.3.106-5 set to be updated
    --> Processing Dependency: libmysqlclient.so.16 for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: php-mysql
    --> Finished Dependency Resolution
    php-mysql-5.3.8-1.el5.art.i386 from installed has depsolving problems
      --> Missing Dependency: libmysqlclient.so.16 is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
    php-mysql-5.3.8-1.el5.art.i386 from installed has depsolving problems
      --> Missing Dependency: libmysqlclient.so.16(libmysqlclient_16) is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
    Error: Missing Dependency: libmysqlclient.so.16(libmysqlclient_16) is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
    Error: Missing Dependency: libmysqlclient.so.16 is needed by package php-mysql-5.3.8-1.el5.art.i386 (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
    The program package-cleanup is found in the yum-utils package.

    .. install failed!


Now updating mysql-server ..

    Installing package(s) with command yum -y install mysql-server ..

    Loaded plugins: fastestmirror
    Loading mirror speeds from cached hostfile
     * Webmin: download.webmin.com
     * atomic: www2.atomicorp.com
     * base: linux.mirrors.es.net
     * extras: mirrors.usc.edu
     * updates: mirrors.usc.edu
    Setting up Install Process
    Resolving Dependencies
    --> Running transaction check
    ---> Package mysql-server.i386 0:5.5.16-1.el5.art set to be updated
    --> Processing Dependency: mysql-libs = 5.5.16-1.el5.art for package: mysql-server
    --> Processing Dependency: mysql = 5.5.16-1.el5.art for package: mysql-server
    --> Processing Dependency: libaio.so.1(LIBAIO_0.4) for package: mysql-server
    --> Processing Dependency: libaio.so.1 for package: mysql-server
    --> Processing Dependency: libaio.so.1(LIBAIO_0.1) for package: mysql-server
    ---> Package mysql-server.x86_64 0:5.5.16-1.el5.art set to be updated
    --> Processing Dependency: libaio.so.1(LIBAIO_0.4)(64bit) for package: mysql-server
    --> Processing Dependency: libaio.so.1(LIBAIO_0.1)(64bit) for package: mysql-server
    --> Processing Dependency: libaio.so.1()(64bit) for package: mysql-server
    --> Running transaction check
    ---> Package libaio.i386 0:0.3.106-5 set to be updated
    ---> Package libaio.x86_64 0:0.3.106-5 set to be updated
    ---> Package mysql.i386 0:5.5.16-1.el5.art set to be updated
    ---> Package mysql.x86_64 0:5.5.16-1.el5.art set to be updated
    --> Processing Dependency: libmysqlclient.so.16 for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16()(64bit) for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: php-mysql
    ---> Package mysql-libs.i386 0:5.5.16-1.el5.art set to be updated
    ---> Package mysql-libs.x86_64 0:5.5.16-1.el5.art set to be updated
    --> Running transaction check
    --> Processing Dependency: libmysqlclient.so.16 for package: php-mysql
    --> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: php-mysql
    ---> Package mysqlclient16.x86_64 0:5.1.57-1.el5.art set to be updated
    --> Finished Dependency Resolution
    php-mysql-5.3.8-1.el5.art.i386 from installed has depsolving problems
      --> Missing Dependency: libmysqlclient.so.16 is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
    php-mysql-5.3.8-1.el5.art.i386 from installed has depsolving problems
      --> Missing Dependency: libmysqlclient.so.16(libmysqlclient_16) is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
    Error: Missing Dependency: libmysqlclient.so.16(libmysqlclient_16) is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
    Error: Missing Dependency: libmysqlclient.so.16 is needed by package php-mysql-5.3.8-1.el5.art.i386 (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
    The program package-cleanup is found in the yum-utils package.

    .. install failed!

[dsoundmn]

I am having the same issue with yum update (not webmin in my case)

Code: Select all

CentOS5 2.6.32.41-1.art.x86_64

I have yum priorities enabled and tried to update with only the asl repo as well.

Code: Select all

Resolving Dependencies
--> Running transaction check
---> Package autofs.x86_64 1:5.0.1-0.rc2.156.el5_7.3 set to be updated
---> Package mysql.i386 0:5.5.16-1.el5.art set to be updated
---> Package mysql.x86_64 0:5.5.16-1.el5.art set to be updated
--> Processing Dependency: libmysqlclient.so.16 for package: php-mysql
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: php-mysql
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: ossec-hids-server
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: php-mysql
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: ossec-hids-server
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: php-mysql
---> Package mysql-libs.i386 0:5.5.16-1.el5.art set to be updated
---> Package mysql-libs.x86_64 0:5.5.16-1.el5.art set to be updated
---> Package mysql-server.i386 0:5.5.16-1.el5.art set to be updated
---> Package mysql-server.x86_64 0:5.5.16-1.el5.art set to be updated
--> Running transaction check
--> Processing Dependency: libmysqlclient.so.16 for package: php-mysql
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: php-mysql
---> Package mysqlclient16.x86_64 0:5.1.56-1.el5.art set to be updated
--> Finished Dependency Resolution
php-mysql-5.3.8-1.el5.art.i386 from installed has depsolving problems
  --> Missing Dependency: libmysqlclient.so.16 is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
php-mysql-5.3.8-1.el5.art.i386 from installed has depsolving problems
  --> Missing Dependency: libmysqlclient.so.16(libmysqlclient_16) is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
Error: Missing Dependency: libmysqlclient.so.16(libmysqlclient_16) is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
Error: Missing Dependency: libmysqlclient.so.16 is needed by package php-mysql-5.3.8-1.el5.art.i386 (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

any thoughts?

[scott]

Are you excluding mysqlclient16 in your config?

[dsoundmn]

Are you excluding mysqlclient16 in your config?

nope, installing mysqlclient16 yields this error - please let me know if you need anything else - i'm on YIM so if you need anything more detailed jump on your user and I'll get in touch.

# yum install mysqlclient16

Code: Select all

Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package mysqlclient16.x86_64 0:5.1.57-1.el5.art set to be updated
--> Finished Dependency Resolution

Dependencies Resolved

=====================================================================================================================================================================================================
 Package                                           Arch                                       Version                                               Repository                                  Size
=====================================================================================================================================================================================================
Installing:
 mysqlclient16                                     x86_64                                     5.1.57-1.el5.art                                      atomic                                     1.8 M

Transaction Summary
=====================================================================================================================================================================================================
Install       1 Package(s)
Upgrade       0 Package(s)

Total download size: 1.8 M
Is this ok [y/N]: y
Downloading Packages:
mysqlclient16-5.1.57-1.el5.art.x86_64.rpm                                                                                                                                     | 1.8 MB     00:01
Running rpm_check_debug
Running Transaction Test
Finished Transaction Test


Transaction Check Error:
  file /usr/lib64/mysql/libmysqlclient.so.16.0.0 from install of mysqlclient16-5.1.57-1.el5.art.x86_64 conflicts with file from package mysql-libs-5.1.59-1.el5.art.x86_64
  file /usr/lib64/mysql/libmysqlclient_r.so.16.0.0 from install of mysqlclient16-5.1.57-1.el5.art.x86_64 conflicts with file from package mysql-libs-5.1.59-1.el5.art.x86_64

[dsoundmn]

could be as simple as just removing and re-installing but i wanted to make sure - another server (RHEL5) upgraded fine this morning give or take the issues in my.cnf

we commented out the following on that one

/usr/libexec/mysqld: unknown variable
'set-variable=local-infile=0'

[scott]

You wouldnt want to install mysqlclient16 with mysql 5.1 on the system. They're the same thing

[dsoundmn]

i figured that much - but that doesn't help with the real issue... anything else you need to check?

[Kalimari]

Hi dsoundmn, edit /etc/my.cnf and check for "skip-locking", if found replace with "skip-external-locking" and start mysql.
Solution from: http://dev.mysql.com/doc/refman/5.5/en/ ... shell.html fixed same issue for me.

[dsoundmn]

Hi dsoundmn, edit /etc/my.cnf and check for "skip-locking", if found replace with "skip-external-locking" and start mysql.
Solution from: http://dev.mysql.com/doc/refman/5.5/en/ ... shell.html fixed same issue for me.

thanks for the extra note - unfortunately the issue is the yum install issue not the unable to start issue :-\

[crnunez]

Hello,
I have the same issue when I tried to upgrade mysql.
My current Mysql: mysql-5.1.59-1.el5.art


[root@ns ~]$ yum update mysupdate mysql mysql-libs mysql-server
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
* atomic: www5.atomicorp.com
* base: mirror.steadfast.net
* centosplus: mirror.raystedman.net
* extras: centos.mirror.lstn.net
* updates: centos.mirror.lstn.net
Setting up Update Process
Resolving Dependencies
--> Running transaction check
---> Package mysql.x86_64 0:5.5.16-2.el5.art set to be updated
--> Processing Dependency: libmysqlclient.so.16 for package: php-mysql
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: php-mysql
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: php-mysql
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: php-mysql
---> Package mysql-libs.i386 0:5.5.16-2.el5.art set to be updated
---> Package mysql-libs.x86_64 0:5.5.16-2.el5.art set to be updated
---> Package mysql-server.x86_64 0:5.5.16-2.el5.art set to be updated
--> Running transaction check
--> Processing Dependency: libmysqlclient.so.16 for package: php-mysql
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16) for package: php-mysql
---> Package mysqlclient16.x86_64 0:5.1.57-1.el5.art set to be updated
--> Finished Dependency Resolution
php-mysql-5.3.8-1.el5.art.i386 from installed has depsolving problems
--> Missing Dependency: libmysqlclient.so.16 is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
php-mysql-5.3.8-1.el5.art.i386 from installed has depsolving problems
--> Missing Dependency: libmysqlclient.so.16(libmysqlclient_16) is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
Error: Missing Dependency: libmysqlclient.so.16(libmysqlclient_16) is needed by package php-mysql-5.3.8-1.el5.art.i386 (installed)
Error: Missing Dependency: libmysqlclient.so.16 is needed by package php-mysql-5.3.8-1.el5.art.i386 (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
The program package-cleanup is found in the yum-utils package.


Do you have any idea about this problem?

[jas8522]

I fixed this dependency issue by removing mysql, mysql-libs, and php-mysql then reinstalling each in that sequence:

https://www.atomicorp.com/forums/viewto ... 823#p31823

You may not need to remove mysql as well (I'd bet this is entirely between mysql-libs and php-mysql), but I figured I may as well get it fixed in one try (just in case it was required as well).

[tkalfaoglu2]

I fixed this dependency issue by removing mysql, mysql-libs, and php-mysql then reinstalling each in that sequence:

https://www.atomicorp.com/forums/viewto ... 823#p31823

You may not need to remove mysql as well (I'd bet this is entirely between mysql-libs and php-mysql), but I figured I may as well get it fixed in one try (just in case it was required as well).

I don't see php-mysql in 5.5, so I'm hesitant to remove the current php-mysql from my system.. Shall I?

[scott]

php-mysql belongs to the php package. It is currently version 5.3.8