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:
Cheers

Once kill gnome panel and re-launch:
Check if it makes any difference.

Thanks for the quick reply. I did your recipe but when i kill gnome-panel
it restarts automtically the same as before.

Well, it sounds some issue with your gnome profile. As a workaround you can try to reset it as:
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:
And then once logout and login again. It will generate new files for gnome setup. It will certainly help you.

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:
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):
Again when i login as root everything is working properly.

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?

Checking disk quota didn't return any outputs whereas "df -k" produced:

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
that will list ALL repo files installed and there state ( on / off )

Yes i've installed some third party repos. Here is the output of "yum repolist all":

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
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 )

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
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


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 ...

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.

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.

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


what ones , i might be able to help if i knew what they were ?

some might be in third party repos

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.

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 .