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Old 05-22-2012, 10:05 AM
Timothy Murphy
 
Default yum problem with glibc

Is anyone getting a yum update problem with glibc and glibc-common?
I'm getting the error message
-------------------------------
Error: Protected multilib versions: glibc-2.12-1.47.el6_2.12.x86_64 !=
glibc-2.12-1.47.el6_2.9.i686
** Found 3 pre-existing rpmdb problem(s), 'yum check' output follows:
bash-4.1.2-9.el6_2.x86_64 is a duplicate with bash-4.1.2-8.el6.centos.x86_64
glibc-common-2.12-1.47.el6_2.12.x86_64 is a duplicate with glibc-
common-2.12-1.47.el6_2.9.x86_64
glibc-common-2.12-1.47.el6_2.12.x86_64 has missing requires of glibc = ('0',
'2.12', '1.47.el6_2.12')
-------------------------------
I've tried "rpm --rebuilddb" but that did not seem to help.

Any suggestions or advice gratefully received.

--
Timothy Murphy
e-mail: gayleard /at/ eircom.net
tel: +353-86-2336090, +353-1-2842366
s-mail: School of Mathematics, Trinity College Dublin


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Old 05-22-2012, 12:29 PM
Johnny Hughes
 
Default yum problem with glibc

On 05/22/2012 05:05 AM, Timothy Murphy wrote:
> Is anyone getting a yum update problem with glibc and glibc-common?
> I'm getting the error message
> -------------------------------
> Error: Protected multilib versions: glibc-2.12-1.47.el6_2.12.x86_64 !=
> glibc-2.12-1.47.el6_2.9.i686
> ** Found 3 pre-existing rpmdb problem(s), 'yum check' output follows:
> bash-4.1.2-9.el6_2.x86_64 is a duplicate with bash-4.1.2-8.el6.centos.x86_64
> glibc-common-2.12-1.47.el6_2.12.x86_64 is a duplicate with glibc-
> common-2.12-1.47.el6_2.9.x86_64
> glibc-common-2.12-1.47.el6_2.12.x86_64 has missing requires of glibc = ('0',
> '2.12', '1.47.el6_2.12')
> -------------------------------
> I've tried "rpm --rebuilddb" but that did not seem to help.
>
> Any suggestions or advice gratefully received.
>

You have both the i686 and x86_64 versions of glibc installed. That
error means that the repo you are trying to update from has a different
version of i686 glibc and x86_64 glibc ... or you are trying to upgrade
one (the x86_64 version) and not the other (the i686 version).

Since multilib installs share some files (all the Documentation, etc.),
that means you must install the same version of each arch if you install
both i686 and x86_64 packages.

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Old 05-23-2012, 09:41 PM
Timothy Murphy
 
Default yum problem with glibc

Johnny Hughes wrote:

>> -------------------------------
>> Error: Protected multilib versions: glibc-2.12-1.47.el6_2.12.x86_64 !=
>> glibc-2.12-1.47.el6_2.9.i686
>> ** Found 3 pre-existing rpmdb problem(s), 'yum check' output follows:
>> bash-4.1.2-9.el6_2.x86_64 is a duplicate with
>> bash-4.1.2-8.el6.centos.x86_64 glibc-common-2.12-1.47.el6_2.12.x86_64 is
>> a duplicate with glibc- common-2.12-1.47.el6_2.9.x86_64
>> glibc-common-2.12-1.47.el6_2.12.x86_64 has missing requires of glibc =
>> ('0', '2.12', '1.47.el6_2.12')
>> -------------------------------
>> I've tried "rpm --rebuilddb" but that did not seem to help.
>>
>> Any suggestions or advice gratefully received.

> You have both the i686 and x86_64 versions of glibc installed. That
> error means that the repo you are trying to update from has a different
> version of i686 glibc and x86_64 glibc ... or you are trying to upgrade
> one (the x86_64 version) and not the other (the i686 version).
>
> Since multilib installs share some files (all the Documentation, etc.),
> that means you must install the same version of each arch if you install
> both i686 and x86_64 packages.

Thank you very much for your response.

But I'm afraid I'm not clear what action I can take.
I don't like to remove any glibc or glibc-common packages,
as I'm afraid it might have a disastrous effect,
since they seem to be required by so many other packages,
including the kernel.

I'm slightly puzzled how the system got in this position,
as I have never said anything except "yum upgrade",
and the repos I have enabled all seem harmless,
though there are several of them:
[adobe-linux-x86_64, CentOS-CR (cr), epel, kbs-CentOS-Extras, rpmforge.

The system (which is in another country) seems to be running fine.
If I leave it will it sort itself out in time?


--
Timothy Murphy
e-mail: gayleard /at/ eircom.net
tel: +353-86-2336090, +353-1-2842366
s-mail: School of Mathematics, Trinity College Dublin


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Old 05-23-2012, 10:04 PM
Johnny Hughes
 
Default yum problem with glibc

On 05/23/2012 04:41 PM, Timothy Murphy wrote:
> Johnny Hughes wrote:
>
>>> -------------------------------
>>> Error: Protected multilib versions: glibc-2.12-1.47.el6_2.12.x86_64 !=
>>> glibc-2.12-1.47.el6_2.9.i686
>>> ** Found 3 pre-existing rpmdb problem(s), 'yum check' output follows:
>>> bash-4.1.2-9.el6_2.x86_64 is a duplicate with
>>> bash-4.1.2-8.el6.centos.x86_64 glibc-common-2.12-1.47.el6_2.12.x86_64 is
>>> a duplicate with glibc- common-2.12-1.47.el6_2.9.x86_64
>>> glibc-common-2.12-1.47.el6_2.12.x86_64 has missing requires of glibc =
>>> ('0', '2.12', '1.47.el6_2.12')
>>> -------------------------------
>>> I've tried "rpm --rebuilddb" but that did not seem to help.
>>>
>>> Any suggestions or advice gratefully received.
>> You have both the i686 and x86_64 versions of glibc installed. That
>> error means that the repo you are trying to update from has a different
>> version of i686 glibc and x86_64 glibc ... or you are trying to upgrade
>> one (the x86_64 version) and not the other (the i686 version).
>>
>> Since multilib installs share some files (all the Documentation, etc.),
>> that means you must install the same version of each arch if you install
>> both i686 and x86_64 packages.
> Thank you very much for your response.
>
> But I'm afraid I'm not clear what action I can take.
> I don't like to remove any glibc or glibc-common packages,
> as I'm afraid it might have a disastrous effect,
> since they seem to be required by so many other packages,
> including the kernel.
>
> I'm slightly puzzled how the system got in this position,
> as I have never said anything except "yum upgrade",
> and the repos I have enabled all seem harmless,
> though there are several of them:
> [adobe-linux-x86_64, CentOS-CR (cr), epel, kbs-CentOS-Extras, rpmforge.
>
> The system (which is in another country) seems to be running fine.
> If I leave it will it sort itself out in time?
>
>

Based on your errors, what I would do is this:

1. You only need 1 version of glibc-common.x86_64. The only way you
could have gotten into this position is either your machine died in the
middle of a yum update or someone force installed the later glibc-common
via the rpm -i command.

I would first try to install the yum-utils package with this command:

yum install yum-utils

once that is installed, I would try:

yum-complete-transaction

If you do not have any incomplete transactions, then you have some bad
packages force installed.

I would figure out exactly what packages I had installed for glibc and
get them all on one version ... you need to be careful with glibc (and
its sub packages) ... it is the most important package on your machine.

How I would do this is that I would download all the RPMs for the latest
version of all the packages you have installed ... for me that would be:

glibc-devel-2.12-1.47.el6_2.12.x86_64.rpm
glibc-headers-2.12-1.47.el6_2.12.x86_64.rpm
glibc-2.12-1.47.el6_2.12.i686.rpm
glibc-common-2.12-1.47.el6_2.12.x86_64.rpm
glibc-2.12-1.47.el6_2.12.x86_64.rpm
nscd-2.12-1.47.el6_2.12.x86_64.rpm

You may have others.

Once I had them all in the same directory, I would try a:

rpm -Uvh *.rpm

then I would look at the errors

based on those errors (if it does not install) then I would likely do:

rpm -Uvh --force *.rpm

that will LIKELY clean up your rpm issues for glibc ... but if you don't
understand the errors, post those here.

2. For bash, I would:

rpm -e bash-4.1.2-8.el6.centos.x86_64

then I would reinstall the other bash

yum reinstall bash-4.1.2-9.el6_2.x86_64

3. The real issue here is to make sure you figure out HOW you got in
this position and how NOT to get into it again.

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Old 05-25-2012, 02:01 PM
Timothy Murphy
 
Default yum problem with glibc

Johnny Hughes wrote:

First, thanks very much for continuing to help me.

> On 05/23/2012 04:41 PM, Timothy Murphy wrote:
>> Johnny Hughes wrote:
>>
>>>> -------------------------------
>>>> Error: Protected multilib versions: glibc-2.12-1.47.el6_2.12.x86_64 !=
>>>> glibc-2.12-1.47.el6_2.9.i686
>>>> ** Found 3 pre-existing rpmdb problem(s), 'yum check' output follows:
>>>> bash-4.1.2-9.el6_2.x86_64 is a duplicate with
>>>> bash-4.1.2-8.el6.centos.x86_64 glibc-common-2.12-1.47.el6_2.12.x86_64
>>>> is a duplicate with glibc- common-2.12-1.47.el6_2.9.x86_64
>>>> glibc-common-2.12-1.47.el6_2.12.x86_64 has missing requires of glibc =
>>>> ('0', '2.12', '1.47.el6_2.12')
>>>> -------------------------------

>>> You have both the i686 and x86_64 versions of glibc installed. That
>>> error means that the repo you are trying to update from has a different
>>> version of i686 glibc and x86_64 glibc ... or you are trying to upgrade
>>> one (the x86_64 version) and not the other (the i686 version).
>>>
>>> Since multilib installs share some files (all the Documentation, etc.),
>>> that means you must install the same version of each arch if you install
>>> both i686 and x86_64 packages.
>> Thank you very much for your response.
>>
>> But I'm afraid I'm not clear what action I can take.
>> I don't like to remove any glibc or glibc-common packages,
>> as I'm afraid it might have a disastrous effect,
>> since they seem to be required by so many other packages,
>> including the kernel.

> Based on your errors, what I would do is this:
>
> 1. You only need 1 version of glibc-common.x86_64. The only way you
> could have gotten into this position is either your machine died in the
> middle of a yum update or someone force installed the later glibc-common
> via the rpm -i command.
>
> I would first try to install the yum-utils package with this command:

I do have this package installed.

> once that is installed, I would try:
>
> yum-complete-transaction

When I run this, an enormous list of packages (I think over 300)
that will be deleted appears, eg
---------------------------------
---> Package kdelibs-common.x86_64 6:4.3.4-11.el6_1.4 will be erased
---> Package kernel.x86_64 0:2.6.32-220.2.1.el6 will be erased
---> Package kernel.x86_64 0:2.6.32-220.4.1.el6 will be erased
---> Package kernel.x86_64 0:2.6.32-220.7.1.el6 will be erased
---> Package kernel.x86_64 0:2.6.32-220.13.1.el6 will be erased
---------------------------------
But before I can answer yes or no, the command fails with
---------------------------------
Error: Trying to remove "yum", which is protected
---------------------------------
I still get this error if I say "yum-complete-transaction --exclude=yum"

> I would figure out exactly what packages I had installed for glibc and
> get them all on one version ... you need to be careful with glibc (and
> its sub packages) ... it is the most important package on your machine.

The only glibc* packages listed in /var/log/yum.* are 64-bit, eg
---------------------------------
[tim@alfred ~]$ sudo grep glibc /var/log/yum*
/var/log/yum.log:Feb 07 02:20:29 Updated: glibc-
common-2.12-1.47.el6_2.5.x86_64
/var/log/yum.log:Feb 07 02:20:45 Updated: glibc-2.12-1.47.el6_2.5.x86_64
...
/var/log/yum.log:Mar 17 17:51:11 Updated: glibc-
common-2.12-1.47.el6_2.9.x86_64
/var/log/yum.log:Mar 17 17:51:24 Updated: glibc-2.12-1.47.el6_2.9.x86_64
...
/var/log/yum.log:May 22 11:38:50 Installed: glibc-2.12-1.47.el6_2.9.x86_64
--------------------------------

I haven't deliberately installed any versions other than these.
This is on a server running CentOS-6.2 (in another country),
and I never say anything relevant on it except "sudo yum update".

> How I would do this is that I would download all the RPMs for the latest
> version of all the packages you have installed ... for me that would be:
>
> glibc-devel-2.12-1.47.el6_2.12.x86_64.rpm
> glibc-headers-2.12-1.47.el6_2.12.x86_64.rpm
> glibc-2.12-1.47.el6_2.12.i686.rpm
> glibc-common-2.12-1.47.el6_2.12.x86_64.rpm
> glibc-2.12-1.47.el6_2.12.x86_64.rpm
> nscd-2.12-1.47.el6_2.12.x86_64.rpm

After "yum-update" the server tried to download the 2.12 versions,
but wasn't able to for the same above reason:

I have them all on another server also running CentOS-6.2:
--------------------------------
[tim@grover ~]$ sudo grep glibc /var/log/yum.log*
...
/var/log/yum.log:May 11 13:58:46 Updated: glibc-
common-2.12-1.47.el6_2.12.x86_64
/var/log/yum.log:May 11 13:59:20 Updated: glibc-2.12-1.47.el6_2.12.x86_64
/var/log/yum.log:May 11 13:59:54 Updated: glibc-
headers-2.12-1.47.el6_2.12.x86_64
/var/log/yum.log:May 11 13:59:59 Updated: glibc-
devel-2.12-1.47.el6_2.12.x86_64
/var/log/yum.log:May 11 14:01:44 Updated: glibc-2.12-1.47.el6_2.12.i686
--------------------------------
so I could copy them from there, and forcefully install them?

> Once I had them all in the same directory, I would try a:
>
> rpm -Uvh *.rpm
>
> then I would look at the errors
>
> based on those errors (if it does not install) then I would likely do:
>
> rpm -Uvh --force *.rpm
>
> that will LIKELY clean up your rpm issues for glibc ... but if you don't
> understand the errors, post those here.

OK, thanks.
I see my other server has not in fact retained copies of these packages,
so I'll collect them separately and try rpm-installing them as you suggest.

I'll let you know if that succeeds or not!

> 3. The real issue here is to make sure you figure out HOW you got in
> this position and how NOT to get into it again.

I think I understand how it occurred.
I tried to yum-remove a package
(I don't remember which one, but it wasn't important)
and I was told that 300+ packages would be removed.
I wasn't sure it I would be asked yes/no to this
(I know now that I will always be asked to approve)
so I stopped the commend with ctrt-C.
Since then I have had these problems.


--
Timothy Murphy
e-mail: gayleard /at/ eircom.net
tel: +353-86-2336090, +353-1-2842366
s-mail: School of Mathematics, Trinity College Dublin


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Old 05-25-2012, 02:43 PM
 
Default yum problem with glibc

Tim,

Timothy Murphy wrote:
> Johnny Hughes wrote:
>> On 05/23/2012 04:41 PM, Timothy Murphy wrote:
>>> Johnny Hughes wrote:
<snip>
>> 3. The real issue here is to make sure you figure out HOW you got in
>> this position and how NOT to get into it again.
>
> I think I understand how it occurred.
> I tried to yum-remove a package
> (I don't remember which one, but it wasn't important)
> and I was told that 300+ packages would be removed.
> I wasn't sure it I would be asked yes/no to this
> (I know now that I will always be asked to approve)
> so I stopped the commend with ctrt-C.
> Since then I have had these problems.

I think you have bigger problems. I don't think that <ctrl-c> out of yum
is the problem.

One dumb question: what's the output of uname -a - *are* you running a
64-bit kernel?

Have you tried yum clean all?

mark

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Old 05-26-2012, 01:16 AM
Timothy Murphy
 
Default yum problem with glibc

m.roth@5-cent.us wrote:

>> I think I understand how it occurred.
>> I tried to yum-remove a package
>> (I don't remember which one, but it wasn't important)
>> and I was told that 300+ packages would be removed.
>> I wasn't sure it I would be asked yes/no to this
>> (I know now that I will always be asked to approve)
>> so I stopped the commend with ctrt-C.
>> Since then I have had these problems.
>
> I think you have bigger problems. I don't think that <ctrl-c> out of yum
> is the problem.
>
> One dumb question: what's the output of uname -a - *are* you running a
> 64-bit kernel?

Thanks for your response.

[tim@alfred glibc]$ uname -a
Linux alfred.gayleard.eu 2.6.32-220.17.1.el6.x86_64 #1 SMP Wed May 16
00:01:37 BST 2012 x86_64 x86_64 x86_64 GNU/Linux

> Have you tried yum clean all?

I have.
More than once.

--
Timothy Murphy
e-mail: gayleard /at/ eircom.net
tel: +353-86-2336090, +353-1-2842366
s-mail: School of Mathematics, Trinity College Dublin


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Old 05-26-2012, 11:45 AM
Timothy Murphy
 
Default yum problem with glibc

Johnny Hughes wrote:

> Based on your errors, what I would do is this:

Thanking you again for all your help.
I have one last question, and then I promise to ask no more!
Could the rpm --force suggestion you make possibly stop the server working?

> 1. You only need 1 version of glibc-common.x86_64.
...
> I would figure out exactly what packages I had installed for glibc and
> get them all on one version ... you need to be careful with glibc (and
> its sub packages) ... it is the most important package on your machine.
>
> How I would do this is that I would download all the RPMs for the latest
> version of all the packages you have installed ... for me that would be:
>
> glibc-devel-2.12-1.47.el6_2.12.x86_64.rpm
> glibc-headers-2.12-1.47.el6_2.12.x86_64.rpm
> glibc-2.12-1.47.el6_2.12.i686.rpm
> glibc-common-2.12-1.47.el6_2.12.x86_64.rpm
> glibc-2.12-1.47.el6_2.12.x86_64.rpm
> nscd-2.12-1.47.el6_2.12.x86_64.rpm

I've downloaded all these to /tmp/glibc/

> Once I had them all in the same directory, I would try a:
>
> rpm -Uvh *.rpm
>
> then I would look at the errors

I get the same error as before:
-----------------------------
[tim@alfred glibc]$ sudo rpm -Uvh *.rpm
error: Failed dependencies:
glibc = 2.12-1.47.el6_2.9 is needed by (installed) glibc-
common-2.12-1.47.el6_2.9.x86_64
-----------------------------

> based on those errors (if it does not install) then I would likely do:
>
> rpm -Uvh --force *.rpm
>
> that will LIKELY clean up your rpm issues for glibc ... but if you don't
> understand the errors, post those here.

Now this is my last question:
Can I be reasonably (say 90%) sure that the above command
will not stop the server running?

The problem is that the server is a long way away (in another country)
and I won't have any way of contacting it if it stops running.

I don't really need to do anything,
as it seems to be running fine as it is -
the update problem doesn't appear to have any deleterious effect.
I can perfectly well leave it until I can deal with the issue on site,
and even re-install CentOS if necessary.

But I guess the problem does raise one general issue,
which maybe others are puzzled by,
and that is why x86_64 and i386 programs are both apparently needed?
Why specifically does glibc-common-2.12-1.47.el6_2.9.x86_64
seem to require glibc-2.12-1.47.el6_2.9, according to the message above?

> 2. For bash, I would:
>
> rpm -e bash-4.1.2-8.el6.centos.x86_64
>
> then I would reinstall the other bash
>
> yum reinstall bash-4.1.2-9.el6_2.x86_64

I've followed your advice for bash,
and seem to have removed this problem at least.


--
Timothy Murphy
e-mail: gayleard /at/ eircom.net
tel: +353-86-2336090, +353-1-2842366
s-mail: School of Mathematics, Trinity College Dublin


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Old 05-26-2012, 01:25 PM
John Stanley
 
Default yum problem with glibc

On Sat, 2012-05-26 at 12:45 +0100, Timothy Murphy wrote:

> Now this is my last question:
> Can I be reasonably (say 90%) sure that the above command
> will not stop the server running?

No you can NOT and don't ever assume that. That's a mistake thinking
that.

> The problem is that the server is a long way away (in another country)
> and I won't have any way of contacting it if it stops running.

Wait and schedule a downtime window for it. That's the heart and soul
of linux. That's playing in the devils den if it's a production
machine.

It's the same in one as the NSS libs on the machine. They break then
you will have to install things by hand. RPM and Yum will not work
period.

If the machine in question has like a Fencing Device (like a drac card )
with an IP addy that's public then maybe (that is card dependent).


John
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Old 05-27-2012, 12:01 AM
Timothy Murphy
 
Default yum problem with glibc

John Stanley wrote:

>> Now this is my last question:
>> Can I be reasonably (say 90%) sure that the above command
>> will not stop the server running?

The command in question was: rpm -Uvh --force *.rpm
where the RPMs were glibc and glibc-common.

> No you can NOT and don't ever assume that.
> That's a mistake thinking that.

Aren't you exaggerating a little?
There are a lot of commands I would feel perfectly safe giving remotely,
eg "sudo yum update" which I've said a couple of times a week
for the last 3 years without any disasters resulting.

The trouble with the command above is that I am not sure
if a change in glibc would affect a running kernel?
I suspect that it would not.

>> The problem is that the server is a long way away (in another country)
>> and I won't have any way of contacting it if it stops running.
>
> Wait and schedule a downtime window for it.

I don't know what a "downtime window" is in this context.
I'm either in the same place as the server, or I am not.

> If the machine in question has like a Fencing Device (like a drac card )
> with an IP addy that's public then maybe (that is card dependent).

I'm not really in that kind of environment.
It isn't the end of the world if the machine goes down;
just a little annoying.

--
Timothy Murphy
e-mail: gayleard /at/ eircom.net
tel: +353-86-2336090, +353-1-2842366
s-mail: School of Mathematics, Trinity College Dublin


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