LinuxQuestions.org
Support LQ: Use code LQ3 and save $3 on Domain Registration
Go Back   LinuxQuestions.org > Forums > Linux Forums > Linux - Distributions > Red Hat
User Name
Password
Red Hat This forum is for the discussion of Red Hat Linux.

Notices

Reply
 
Search this Thread
Old 01-26-2013, 01:30 AM   #1
mansourk
LQ Newbie
 
Registered: Jan 2013
Posts: 8

Rep: Reputation: Disabled
Problems as non-root user


Hi All,

Recently i installed Centos 6 with Gnome on my PC and later on updated it to version 6.3, everything was fine at the beggining, but then i've got these problems: I can't run some apps like evince and when i try to run it from terminal i get segmentation fault error. or when i click on System tab in Gnome-system-monitor it crashes. Some of the gnome panel applets like trash, clock, desktop switcher has been disappeared from my gnome-panel and when i click on "Add to panel" nothing happens and the applets list doesn't show up. I also installed Openbox but when i choose it on login screen i get a black screen for a few seconds and get back to login screen again.
The things are OK when i login as root; i can login to Openbox, and when i login to Gnome the gnome panel is alright and i can run evince... It looks like some permission issue, but i can't figure it out. I don't know if that's relevant but i changed my root password with "passwd" to my regular-account/sudo password at some point.
This is what i got when i issued "uname -a" in terminal:
Code:
Linux dhcppc0 2.6.32-279.19.1.el6.x86_64 #1 SMP Wed Dec 19 07:05:20 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
Cheers
 
Old 01-26-2013, 01:42 AM   #2
shivaa
Senior Member
 
Registered: Jul 2012
Location: Grenoble, Fr.
Distribution: Sun Solaris, RHEL, Ubuntu, Debian 6.0
Posts: 1,797
Blog Entries: 4

Rep: Reputation: 285Reputation: 285Reputation: 285
Once kill gnome panel and re-launch:
Code:
~$ ps -Af | grep gnome-panel
~$ kill -9 <pid>
~$ gnome-panel &
Check if it makes any difference.
 
Old 01-26-2013, 06:28 AM   #3
mansourk
LQ Newbie
 
Registered: Jan 2013
Posts: 8

Original Poster
Rep: Reputation: Disabled
Thanks for the quick reply. I did your recipe but when i kill gnome-panel
it restarts automtically the same as before.
 
Old 01-26-2013, 07:11 AM   #4
shivaa
Senior Member
 
Registered: Jul 2012
Location: Grenoble, Fr.
Distribution: Sun Solaris, RHEL, Ubuntu, Debian 6.0
Posts: 1,797
Blog Entries: 4

Rep: Reputation: 285Reputation: 285Reputation: 285
Well, it sounds some issue with your gnome profile. As a workaround you can try to reset it as:
Code:
~$ ls -la | egrep ".gno|.gcon"
It will list out your gnome setup files like .gnome, .gnome2, .gconf, .gconfd etc. for your profile.
So move all 5 or 6 files into some directory, as:
Code:
~$ mkdir ~/gnome_archive
~$ mv .gnome .gnome2 .gconf .gconfd ~/gnome_archive
And then once logout and login again. It will generate new files for gnome setup. It will certainly help you.
 
Old 01-26-2013, 08:53 AM   #5
mansourk
LQ Newbie
 
Registered: Jan 2013
Posts: 8

Original Poster
Rep: Reputation: Disabled
I did reset my gnome profile as you said, but still i'm having the problems in my gnome
session. After i logged in again i listed my gnome setup files:
Code:
[mansour@dhcppc3 ~]$ ls -la | egrep ".gno|.gcon"
drwx------.  4 mansour mansour  4096 Jan 26 16:54 .gconf
drwx------.  2 mansour mansour  4096 Jan 26 16:57 .gconfd
drwx------.  6 mansour mansour  4096 Jan 26 16:55 .gnome2
drwx------.  2 mansour mansour  4096 Jan 26 16:55 .gnome2_private
drwxrwxr-x.  7 mansour mansour  4096 Jan 26 16:51 gnome_archive
They are not exactly the same as yours but i dont know if that's the problem.
I'm still seeing more problems, for example in the "Apearance preferences" window when
i click on Background tab the window crashes.
I'm also not able to open pdf files with evince by double clicking on them. I tried launching evince from terminal, it only worked with sudo (although it gives a warning):
Code:
]$ evince
Segmentation fault
 $ sudo evince
** (evince:5218): WARNING **: Failed to create dbus proxy for org.gnome.SettingsDaemon: Could not get owner of name 'org.gnome.SettingsDaemon': no such name
Again when i login as root everything is working properly.
 
Old 01-26-2013, 09:17 AM   #6
shivaa
Senior Member
 
Registered: Jul 2012
Location: Grenoble, Fr.
Distribution: Sun Solaris, RHEL, Ubuntu, Debian 6.0
Posts: 1,797
Blog Entries: 4

Rep: Reputation: 285Reputation: 285Reputation: 285
No need to alter gnome files anymore. Application crashes may happen because of low disk or user quota issue.

Can you once check your user quota (if applicable) and disk space?
Code:
~$ quota <uername>
~$ df -k

Last edited by shivaa; 01-26-2013 at 09:21 AM.
 
Old 01-26-2013, 12:16 PM   #7
mansourk
LQ Newbie
 
Registered: Jan 2013
Posts: 8

Original Poster
Rep: Reputation: Disabled
Checking disk quota didn't return any outputs whereas "df -k" produced:
Code:
Filesystem           1K-blocks      Used Available Use% Mounted on
/dev/mapper/vg_karami-lv_root
                      51606140   3413740  47668332   7% /
tmpfs                   763756       124    763632   1% /dev/shm
/dev/sda1               495844     53300    416944  12% /boot
/dev/mapper/vg_karami-lv_home
                      21778996   3922536  16750132  19% /home
 
Old 01-26-2013, 03:40 PM   #8
John VV
Guru
 
Registered: Aug 2005
Posts: 13,446

Rep: Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797
by chance did you install third party repos ?
like say rpmforge ? or epel ? or ELrepo ? or some other


some repos have incompatible rpm's in them
because of this the yum plugin "yum-priorities" needs to be installed AND CONFIGURED

can you post the output of this
Code:
su -
yum repolist all
that will list ALL repo files installed and there state ( on / off )
 
Old 01-26-2013, 11:29 PM   #9
mansourk
LQ Newbie
 
Registered: Jan 2013
Posts: 8

Original Poster
Rep: Reputation: Disabled
Yes i've installed some third party repos. Here is the output of "yum repolist all":
Code:
Loaded plugins: fastestmirror, refresh-packagekit
Loading mirror speeds from cached hostfile
epel/metalink                                            | 4.4 kB     00:00     
 * base: ftp.ntua.gr
 * epel: ftp.riken.jp
 * extras: ftp.ntua.gr
 * rpmforge: mirror.de.leaseweb.net
 * updates: ftp.ntua.gr
base                                                     | 3.7 kB     00:00     
extras                                                   | 3.5 kB     00:00     
rpmforge                                                 | 1.9 kB     00:00     
updates                                                  | 3.5 kB     00:00     
repo id                repo name                                  status
C6.0-base              CentOS-6.0 - Base                          disabled
C6.0-centosplus        CentOS-6.0 - CentOSPlus                    disabled
C6.0-contrib           CentOS-6.0 - Contrib                       disabled
C6.0-extras            CentOS-6.0 - Extras                        disabled
C6.0-updates           CentOS-6.0 - Updates                       disabled
C6.1-base              CentOS-6.1 - Base                          disabled
C6.1-centosplus        CentOS-6.1 - CentOSPlus                    disabled
C6.1-contrib           CentOS-6.1 - Contrib                       disabled
C6.1-extras            CentOS-6.1 - Extras                        disabled
C6.1-updates           CentOS-6.1 - Updates                       disabled
C6.2-base              CentOS-6.2 - Base                          disabled
C6.2-centosplus        CentOS-6.2 - CentOSPlus                    disabled
C6.2-contrib           CentOS-6.2 - Contrib                       disabled
C6.2-extras            CentOS-6.2 - Extras                        disabled
C6.2-updates           CentOS-6.2 - Updates                       disabled
base                   CentOS-6 - Base                            enabled: 6,346
c6-media               CentOS-6 - Media                           disabled
centosplus             CentOS-6 - Plus                            disabled
contrib                CentOS-6 - Contrib                         disabled
debug                  CentOS-6 - Debuginfo                       disabled
epel                   Extra Packages for Enterprise Linux 6 - x8 enabled: 8,326
epel-debuginfo         Extra Packages for Enterprise Linux 6 - x8 disabled
epel-source            Extra Packages for Enterprise Linux 6 - x8 disabled
epel-testing           Extra Packages for Enterprise Linux 6 - Te disabled
epel-testing-debuginfo Extra Packages for Enterprise Linux 6 - Te disabled
epel-testing-source    Extra Packages for Enterprise Linux 6 - Te disabled
extras                 CentOS-6 - Extras                          enabled:    17
google-chrome          google-chrome - 64-bit                     disabled
remi                   Les RPM de remi pour Enterprise Linux 6 -  disabled
remi-test              Les RPM de remi en test pour Enterprise Li disabled
rpmforge               RHEL 6 - RPMforge.net - dag                enabled: 4,458
rpmforge-extras        RHEL 6 - RPMforge.net - extras             disabled
rpmforge-testing       RHEL 6 - RPMforge.net - testing            disabled
tor                    Tor experimental repo                      disabled
tor-source             Tor experimental source repo               disabled
updates                CentOS-6 - Updates                         enabled: 1,092
repolist: 20,239
 
Old 01-27-2013, 12:11 AM   #10
John VV
Guru
 
Registered: Aug 2005
Posts: 13,446

Rep: Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797
no wonder you are having problems
you still have cent 0 & 1 & 2 repo files present, disabled but still in the yum.repo.d folder

CentOS 6.3 is the current
Quote:
base CentOS-6 - Base enabled: 6,346 -- GOOD
updates CentOS-6 - Updates enabled: 1,092 -- GOOD
epel Extra Packages for Enterprise Linux 6 - x8 enabled: 8,326 -- might need yum-priorities installed
rpmforge RHEL 6 - RPMforge.net - dag enabled: 4,458 -- NEEDS yum-priorities installed
rpmforge is causing some problems most likely

though RPMforge has gone to great length to get compatible with the base and updates repos , it still can change some BASE system files over to rpmforge . When that happens the base abd updates and epel become incompatible

the issue IS a lot better that it was/ is in centos5 but it is still there .


remi also will cause problems when mixed in with ( rpmforge & epel )
Quote:
Suggest caution if using this repo due to replacement of core packages.

the "seg faults" are a common issue with missed matched rpm's installed from incompatible repos

depending on just what was installed from where and how many packages ( and what they are ) it ? might ? be fixable
-- no guaranties !!! ---

i would first start with uninstalling every rpmforge rpm
Code:
su -
rpm -qa | grep rf
will output a list from RPMforge
then disable the rpmforge repo
( in the case of system files replaced with rpm's from the updates and base )
then uninstall all "rf" rpm's

then run " yum update"
using ONLY the base and update repos

-- no guaranties !!! ---

if that works and you still have a working system ( you might NOT )
install the yum plugin and configure it
http://wiki.centos.org/PackageManagement/Yum/Priorities

then do the same for remi
SEE: the warning on the centos wiki
http://wiki.centos.org/AdditionalResources/Repositories
Quote:
Suggest caution if using this repo due to replacement of core packages.


then add back in ( guessing multimedia rpms ) the programs from rpmforge
-- with yum-priorities running , that will stop base system programs from being replaced

--- note ---

It might be much faster to do a new clean install of centos 6.3 from the dvd
if you have a good back up of your data than trying to fix it

if only a few ,say12 or so, base packages were replaced it is fixable
might take a day or 3 ...

Last edited by John VV; 01-27-2013 at 12:18 AM.
 
1 members found this post helpful.
Old 01-27-2013, 08:50 AM   #11
mansourk
LQ Newbie
 
Registered: Jan 2013
Posts: 8

Original Poster
Rep: Reputation: Disabled
Thank you, John, for your complete reply. Looks like i've screwed up things quite badly. I reckon i'd go for a clean install since it'd save me some headaches, but this time i'd be much more cautious with third party repos. Thanks everybody for kind replies, i learned a good deal from you.
 
Old 02-01-2013, 07:47 AM   #12
mansourk
LQ Newbie
 
Registered: Jan 2013
Posts: 8

Original Poster
Rep: Reputation: Disabled
Finally i found the cause of that issue. As John suggested it was a problem of incompatible rpms, and it was
caused by installing "zlib" package from source while an older version of it was already installed on my system.
I found this after making a fresh CentOS 6.3 installation, and getting the same issues after i installed a bunch of
scientific packages from source.
 
Old 02-01-2013, 02:06 PM   #13
John VV
Guru
 
Registered: Aug 2005
Posts: 13,446

Rep: Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797
Quote:
I found this after making a fresh CentOS 6.3 installation, and getting the same issues after i installed a bunch of
scientific packages from source.
if you neet newer versions of some programs you can build the source
BUY do not !!! install it to /usr !!!!

instead use a build folder
like the install folder for the program that NEEDS a newer version of the program as a prerequisite, and do NOT put that folder in the system $PATH

for example

the development gimp 2.9

make a folder called /opt/gimp2.9

on cent this would need EVERYTHING and EVERY prerequisite built

---To use just one as an example ----

the current testing gtk

pass "/opt/gipm2.9/gtk as the "--prefix=" install location in building gkt
then pass that build folder to gimp for
$LD_LIBRARY_PATH
$PKG_CONFIG_PATH
and others to the build line


this is where a build script can come in handy to run configure and make

for more than one or two dependencies it becomes very complex


Quote:
i installed a bunch of
scientific packages from source.
what ones , i might be able to help if i knew what they were ?

some might be in third party repos

Last edited by John VV; 02-01-2013 at 02:07 PM.
 
Old 02-01-2013, 11:39 PM   #14
mansourk
LQ Newbie
 
Registered: Jan 2013
Posts: 8

Original Poster
Rep: Reputation: Disabled
Thank you, John. I uninstaled the zlib package which i had installed from source and for now everything seems
to work alright, I had installed it in /usr/local and it was screwing with my system. I have also installed "szip"
and "HDF5" in /usr/local which for now havn't caused any problems. Thanks for the instructions, it's extremely usefull for me because i get to install many packages from source.
 
Old 02-02-2013, 12:23 AM   #15
John VV
Guru
 
Registered: Aug 2005
Posts: 13,446

Rep: Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797Reputation: 1797
i tend to build from source a lot of things
some just because i have been building them for 10 years and it is a " no brainer" to do

BUT if one of the prerequisites needs something newer ( or older ) than is in the system
the operating system must not see it or at least see it AFTER the version that is default

This can lead to some odd problems if one makes a "oops" and installs a conflicting program like say "glib"
the Gimp example i used often needs a newer version than even the current fedora might have

In your case it was zlib so not to much damage and it was in /usr/local

it takes time to learn the "ins and outs" so just make sure you do learn from the mistakes , then learn from the all new, new ones you WILL make .
 
  


Reply


Thread Tools Search this Thread
Search this Thread:

Advanced Search

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is Off
HTML code is Off


Similar Threads
Thread Thread Starter Forum Replies Last Post
[SOLVED] Problems with su, sudo, root and user bwgolling Slackware 10 06-02-2011 03:28 PM
mount. root rw:ok. user rw problems nullnill Linux - Networking 2 02-09-2009 07:36 AM
MySQL Root User problems nitro_punk85 Linux - Server 2 10-17-2007 09:52 PM
user problems, have to login as root!! desperate_penguin Linux - Software 1 11-26-2005 10:13 AM
Non-root user problems natto34 Linux - General 1 07-16-2002 02:41 PM


All times are GMT -5. The time now is 09:32 PM.

Main Menu
Advertisement
My LQ
Write for LQ
LinuxQuestions.org is looking for people interested in writing Editorials, Articles, Reviews, and more. If you'd like to contribute content, let us know.
Main Menu
Syndicate
RSS1  Latest Threads
RSS1  LQ News
Twitter: @linuxquestions
identi.ca: @linuxquestions
Facebook: linuxquestions Google+: linuxquestions
Open Source Consulting | Domain Registration