yum and rpm Dependency trouble

aoscott · 04-25-2013, 04:25 PM

I'm trying to setup mysql on a server and am getting what looks like dependency conflicts. This server was preinstalled with different utilities including anti virus, monitoring. Looks like many of these used libraries for i386, i686 and x86_64. Is there a way to clean up this mess or should the system be completely rebuilt?

Code:

Error: Protected multilib versions: openssl-1.0.0-20.el6_2.5.i686 != openssl-1.0.0-27.el6_4.2.x86_64
Error: Protected multilib versions: mysql-libs-5.1.61-4.el6.i686 != mysql-libs-5.1.67-1.el6_3.x86_64

chrism01 · 04-25-2013, 08:21 PM

Show

Code:

cat /etc/*release*
uname -a
yum repolist

Hint: if you've got any repos other than the official ones enabled, you must install set yum-priorities http://wiki.centos.org/PackageManagement/Yum/Priorities to protect your system from inter-repo conflicts.

John VV · 04-25-2013, 10:27 PM

el6
so is this a RHEL6.4 or CentOS 6.4 or a SL6.4 install

chrism01's 3 commands will show all this

1) the version of the os
2) the kernel running
3) the repos that are turned on

though a few repos ARE recommended to be turned off and ONLY turned on for the one time for installing something
so i would use

Code:

su -
yum repolist all

that will show everything and if it is on or off

normally the only easy way to fix a 32 bit VS 64 bit conflict is to uninstall the 32 bit then install the new 64 bit and the new 32 bit that gos with the 64 bit version ( if you NEED the 32 bit version also )

something like this -- but with mysql there will be dependencies

Code:

su -
yum remove  mysql-libs-5.1.61-4
yum install mysql-libs

the second will install the 64 bit by default

aoscott · 04-25-2013, 11:33 PM

This is RHEL 6.3. I believe the only repo configured is my company's RHN satellite REPO but I will double check.

aoscott · 04-26-2013, 01:01 PM

I found one additional repo

Code:

 yum repolist
Loaded plugins: product-id, refresh-packagekit, rhnplugin, security, subscription-manager
Updating certificate-based repositories.
Unable to read consumer identity
repo id                                        repo name                                      status
rhel6u3_only                                   rhel6u3_only                                   3,653
rhel6u3tools                                   rhel6u3tools                                      64
repolist: 3,717

I renamed the repo in

Code:

/etc/yum.repos.d

Then I ran

Code:

yum clean all

Attempted to install mysql and got the same result with library conflicts.

aoscott · 04-26-2013, 01:22 PM

Your direction was one that I didn't do after making the change to my repos. The version of mysql-libs was installed and it was x86_64. I removed it and it was removed cleanly. Then I attempted to install mysql. This time it installed without flaw.

Thanks again!

John VV · 04-26-2013, 01:37 PM

it is likely there will be more conflicts
the 32 bit "mysql-libs" also needs the matching
glibc.i686
openssl.i686
zlib.i686

so there might still be a mismatching glibc.i686
check it !
compare the two outputs of this

Code:

yum info glibc.i686
----- with this output ----
yum info glibc.x86_64

if they match , that is good . If not..... not good

aoscott · 04-26-2013, 01:42 PM

Alright here is the output from both. They are both installed. Will this create problems in the future? Which part needs to match?

Code:

# yum info glibc.i686
Loaded plugins: product-id, rhnplugin, security, subscription-manager
Updating certificate-based repositories.
Unable to read consumer identity
Installed Packages
Name        : glibc
Arch        : i686
Version     : 2.12
Release     : 1.107.el6
Size        : 13 M
Repo        : installed
From repo   : rhel-x86_64-server-6
Summary     : The GNU libc libraries
URL         : http://sources.redhat.com/glibc/
License     : LGPLv2+ and LGPLv2+ with exceptions and GPLv2+
Description : The glibc package contains standard libraries which are used by
            : multiple programs on the system. In order to save disk space and
            : memory, as well as to make upgrading easier, common system code is
            : kept in one place and shared between programs. This particular package
            : contains the most important sets of shared libraries: the standard C
            : library and the standard math library. Without these two libraries, a
            : Linux system will not function.

Code:

# yum info glibc.x86_64
Loaded plugins: product-id, rhnplugin, security, subscription-manager
Updating certificate-based repositories.
Unable to read consumer identity
Installed Packages
Name        : glibc
Arch        : x86_64
Version     : 2.12
Release     : 1.107.el6
Size        : 12 M
Repo        : installed
From repo   : rhel-x86_64-server-6
Summary     : The GNU libc libraries
URL         : http://sources.redhat.com/glibc/
License     : LGPLv2+ and LGPLv2+ with exceptions and GPLv2+
Description : The glibc package contains standard libraries which are used by
            : multiple programs on the system. In order to save disk space and
            : memory, as well as to make upgrading easier, common system code is
            : kept in one place and shared between programs. This particular package
            : contains the most important sets of shared libraries: the standard C
            : library and the standard math library. Without these two libraries, a
            : Linux system will not function.

John VV · 04-26-2013, 02:54 PM

Code:

Version     : 2.12
Release     : 1.107.el6

both are the same so that is good

just be on the look out for any more

it looks like this was a simple issue ( lucky)

aoscott · 04-26-2013, 04:05 PM

Is it better practice use yum to install individual rpm packages rather than rpm -i to avoid dependency issues? Also use the same method with yum to remove packages instead of rpm -e?

John VV · 04-26-2013, 04:22 PM

yum resolves the dependencies rpm dose NOT
with rpm you can install an incompatible version and if you are unlucky -- never boot the system ever again

yum is WAY SAFER !!!

only use "rpm" as a last resort or for some things
a good example is installing libreoffice4
you use rpm for that , because it is a stand alone program

see the yum help and man page

Code:

su -
yum --help
--- and this ---
man yum

aoscott · 04-26-2013, 06:07 PM

Seems like a rookie mistake on my part. I have been installing rpms using rpm only to have to hunt down a myriad of dependencies.

aoscott · 04-26-2013, 07:46 PM

Unfortunately ran into another problem. So my dependency issues are not resolved yet. I was trying to build and compile a few installations of various softwares. Discovered that gcc was not installed on this server.

Ran

Code:

yum install gcc

Got this output indicating an issue with glibc once again.

Code:

# yum install gcc
Loaded plugins: product-id, rhnplugin, security, subscription-manager
Updating certificate-based repositories.
Unable to read consumer identity
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package gcc.x86_64 0:4.4.6-4.el6 will be installed
--> Processing Dependency: cpp = 4.4.6-4.el6 for package: gcc-4.4.6-4.el6.x86_64
--> Processing Dependency: libgomp = 4.4.6-4.el6 for package: gcc-4.4.6-4.el6.x86_64
--> Processing Dependency: cloog-ppl >= 0.15 for package: gcc-4.4.6-4.el6.x86_64
--> Processing Dependency: glibc-devel >= 2.2.90-12 for package: gcc-4.4.6-4.el6.x86_64
--> Processing Dependency: libgomp.so.1()(64bit) for package: gcc-4.4.6-4.el6.x86_64
--> Running transaction check
---> Package cloog-ppl.x86_64 0:0.15.7-1.2.el6 will be installed
--> Processing Dependency: libppl.so.7()(64bit) for package: cloog-ppl-0.15.7-1.2.el6.x86_64
--> Processing Dependency: libppl_c.so.2()(64bit) for package: cloog-ppl-0.15.7-1.2.el6.x86_64
---> Package cpp.x86_64 0:4.4.6-4.el6 will be installed
--> Processing Dependency: libmpfr.so.1()(64bit) for package: cpp-4.4.6-4.el6.x86_64
---> Package glibc-devel.x86_64 0:2.12-1.80.el6 will be installed
--> Processing Dependency: glibc-headers = 2.12-1.80.el6 for package: glibc-devel-2.12-1.80.el6.x86_64
--> Processing Dependency: glibc = 2.12-1.80.el6 for package: glibc-devel-2.12-1.80.el6.x86_64
--> Processing Dependency: glibc-headers for package: glibc-devel-2.12-1.80.el6.x86_64
---> Package libgomp.x86_64 0:4.4.6-4.el6 will be installed
--> Running transaction check
---> Package glibc.i686 0:2.12-1.80.el6 will be installed
--> Processing Dependency: glibc-common = 2.12-1.80.el6 for package: glibc-2.12-1.80.el6.i686
--> Processing Dependency: libfreebl3.so(NSSRAWHASH_3.12.3) for package: glibc-2.12-1.80.el6.i686
--> Processing Dependency: libfreebl3.so for package: glibc-2.12-1.80.el6.i686
---> Package glibc-headers.x86_64 0:2.12-1.80.el6 will be installed
--> Processing Dependency: kernel-headers >= 2.2.1 for package: glibc-headers-2.12-1.80.el6.x86_64
--> Processing Dependency: kernel-headers for package: glibc-headers-2.12-1.80.el6.x86_64
---> Package mpfr.x86_64 0:2.4.1-6.el6 will be installed
---> Package ppl.x86_64 0:0.10.2-11.el6 will be installed
--> Running transaction check
---> Package glibc.i686 0:2.12-1.80.el6 will be installed
--> Processing Dependency: glibc-common = 2.12-1.80.el6 for package: glibc-2.12-1.80.el6.i686
---> Package kernel-headers.x86_64 0:2.6.32-279.el6 will be installed
---> Package nss-softokn-freebl.i686 0:3.12.9-11.el6 will be installed
--> Finished Dependency Resolution
Error: Package: glibc-2.12-1.80.el6.i686 (rhel6u3_only)
           Requires: glibc-common = 2.12-1.80.el6
           Installed: glibc-common-2.12-1.107.el6.x86_64 (@rhel-x86_64-server-6)
               glibc-common = 2.12-1.107.el6
           Available: glibc-common-2.12-1.80.el6.x86_64 (rhel6u3_only)
               glibc-common = 2.12-1.80.el6
 You could try using --skip-broken to work around the problem
 You could try running: rpm -Va --nofiles --nodigest

I tried to uninstall these but it looks like quite a few things rely on glibc including yum.

John VV · 04-26-2013, 08:41 PM

you are going to have to clear out all the old and bad mismatched rpms in the satellite repo

this is going to NEED red hat tech support

it is possible to weed out this tangled mess
but it will take 2 to 4 weeks

reinstalling from a up to date repo will take 30 min.

Time to call red hat !

the old version of gcc in your local repo wants to use
"glibc-common = 2.12-1.80.el6"
but the newer version of
"glibc-common = 2.12-1.107.el6"
is what is installed

Quote:

I tried to uninstall these but it looks like quite a few things rely on glibc including yum.

glibc is basically the operating system

aoscott · 04-27-2013, 11:37 AM

Thanks again. I had a feeling that might be the issue. It looks like my company provisioned this VM with a version of RHEL and connected to a satellite RHN repo that is out of date. Could that be the issue?