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Old 10-21-2011, 07:38 AM
Mikko Koivunen
 
Default Missing stuff in /bin

Hi all

Having a weird issue with CentOS 6. I lost a lot of stuff in /bin/
(cp,rpm,cat and others) on one host, but that was a development
machine and I'm not really sure what happened there.

But now I ran into a similar problem (missing at least /bin/vi and
/bin/cp) on a host where I'm a lot more certain of all that has been
done on the machine.

This is what happened, it's a _complete_ list of what I have done on the host:

- installed centos 6 from dvd .iso, into esxi 4.1 vm
- selected "web server" as base packages in install
- configured network interface
- configured some variables in /etc/profile.d (with vi - note this later)
- installed mysqld and some php packages
- created a backup script in /etc/cron.daily (just does mysqldump and
/var/www gzip'ing)
- removed postgresql
- put some data in mysql db + apache documentroot
- ran yum update
- tried to configure an apache virtualhost - noticed that vi is missing
- noticed that /bin/cp is missing as well
- coreutils & vim-minimal are installed according to rpm

Yum.log shows that during the yum update vim-minimal was updated,
coreutils not, no package removals visible. Can't see anything in
dmesg, root's history, /var/log/secure, /var/log/messages that would
explain this. No one else has access.

I am certain I have not accidentally removed the files.. Anyone seen
anything similar? I'm a bit hesitant to say it's a bug or claim that
yum update is to blame, because then I'd think a lot of folks were
bitten by similar problems.

regards
Mikko Koivunen
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Old 10-21-2011, 02:04 PM
John Doe
 
Default Missing stuff in /bin

From: Mikko Koivunen <mikko.koivunen@gmail.com>

> Having a weird issue with CentOS 6. I lost a lot of stuff in /bin/
> (cp,rpm,cat and others) on one host, but that was a development
> machine and I'm not really sure what happened there.
>
> - coreutils & vim-minimal are installed according to rpm

Do you miss all coreutils files or just a few...?
rpm -qV coreutils

How did you remove postgresql...?
rpm -e or yum remove?

JD
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Old 10-21-2011, 02:39 PM
Les Mikesell
 
Default Missing stuff in /bin

On Fri, Oct 21, 2011 at 9:04 AM, John Doe <jdmls@yahoo.com> wrote:
>
>> Having a weird issue with CentOS 6. I lost a lot of stuff in /bin/
>> (cp,rpm,cat and others) on one host, but that was a development
>> machine and I'm not really sure what happened there.
>>
>> - coreutils & vim-minimal are installed according to rpm
>
> Do you miss all coreutils files or just a few...?
> rpm -qV coreutils
>
> How did you remove postgresql...?
> rpm -e or yum remove?
>

This sounds like a local problem. 'rpm -Va' should show everything
that differs from the packages that should be installed and you can
use 'yum reinstall' to fix them up. Not sure if there is a handy way
to see the packages the damaged/missing files belong to all at once,
but 'rpm -q --whatprovides /path/to/file' will check individually.

--
Les Mikesell
lesmikesell@gmail.com
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Old 10-21-2011, 03:38 PM
Mikko Koivunen
 
Default Missing stuff in /bin

On Fri, Oct 21, 2011 at 5:04 PM, John Doe <jdmls@yahoo.com> wrote:
> From: Mikko Koivunen <mikko.koivunen@gmail.com>
>> Having a weird issue with CentOS 6. I lost a lot of stuff in /bin/
>> - coreutils & vim-minimal are installed according to rpm
> Do you miss all coreutils files or just a few...?
> rpm -qV coreutils

Good tip on the -qV option. It shows I am missing: basename, chown,
cp, dd, false, pwd, rm, sync, touch

> How did you remove postgresql...?
> rpm -e or yum remove?

Yum remove, /var/log/yum.log shows postgresql "erased", no other
packages removed.

- Mikko
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Old 10-21-2011, 04:07 PM
Mikko Koivunen
 
Default Missing stuff in /bin

On Fri, Oct 21, 2011 at 5:39 PM, Les Mikesell <lesmikesell@gmail.com> wrote:
> On Fri, Oct 21, 2011 at 9:04 AM, John Doe <jdmls@yahoo.com> wrote:
>>> Having a weird issue with CentOS 6. I lost a lot of stuff in /bin/
>>> - coreutils & vim-minimal are installed according to rpm
> This sounds like a local problem. *'rpm -Va' should show everything
> that differs from the packages that should be installed and you can
> use 'yum reinstall' to fix them up. *Not sure if there is a handy way
> to see the packages the damaged/missing files belong to all at once,
> but 'rpm -q --whatprovides /path/to/file' will check individually.

Thanks. I'll try to reinstall them, but I am a bit nervous because I
don't see how this has happened.

For reference, here's the output from rpm -Va:

missing /bin/plymouth
S.5....T. c /etc/maven/maven2-depmap.xml
S.5....T. c /etc/ssh/sshd_config
missing /bin/mountpoint
missing /bin/red
S.5....T. c /etc/pki/nssdb/pkcs11.txt
S.5....T. c /etc/nslcd.conf
missing /bin/dbus-daemon
missing /bin/vi
....L.... c /etc/pam.d/fingerprint-auth
....L.... c /etc/pam.d/password-auth
....L.... c /etc/pam.d/smartcard-auth
....L.... c /etc/pam.d/system-auth
missing /bin/tracepath
missing /bin/cgexec
missing /bin/cgset
S.5....T. c /etc/httpd/conf/httpd.conf
missing /bin/unicode_stop
missing /bin/nano
missing /bin/setserial
missing /bin/basename
missing /bin/chown
missing /bin/cp
missing /bin/dd
missing /bin/false
missing /bin/pwd
missing /bin/rm
missing /bin/sync
missing /bin/touch
missing /bin/kill
missing /bin/raw
..5....T. c /usr/lib/security/classpath.security


- Mikko
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Old 10-21-2011, 04:55 PM
 
Default Missing stuff in /bin

Mikko Koivunen wrote:
> On Fri, Oct 21, 2011 at 5:04 PM, John Doe <jdmls@yahoo.com> wrote:
>> From: Mikko Koivunen <mikko.koivunen@gmail.com>
>>> Having a weird issue with CentOS 6. I lost a lot of stuff in /bin/
>>> - coreutils & vim-minimal are installed according to rpm
>> Do you miss all coreutils files or just a few...?
>> rpm -qV coreutils
>
> Good tip on the -qV option. It shows I am missing: basename, chown,
> cp, dd, false, pwd, rm, sync, touch
>
>> How did you remove postgresql...?
>> rpm -e or yum remove?
>
> Yum remove, /var/log/yum.log shows postgresql "erased", no other
> packages removed.

Maybe it's time to check for rootkits?

mark

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