oracle linux 5.8 64bit

since applying these updates:
Feb 12 09:14:12 Updated: elinks-0.11.1-8.el5_9.x86_64
Feb 12 09:14:13 Installed: kernel-uek-firmware-2.6.32-300.39.4.el5uek.noarch
Feb 12 09:14:26 Installed: kernel-uek-2.6.32-300.39.4.el5uek.x86_64
Feb 12 21:23:10 Updated: nss_ldap-253-51.el5_9.1.x86_64
Feb 12 21:23:11 Updated: nss_ldap-253-51.el5_9.1.i386

when using the gnome interface there are a number of things that root can no longer do. when i click on the editor icon(gedit), nothing happens, if i click on the software update (applications >> system tools >> software update), it asks me for the root password, which it never did before. if i try to access the .bash_profile or the /var/log/messages files i get a message that i don't have the permissions necessary to open the file.. i can invoke a terminal session and use vi to access those files.

i have 5 linux servers, only two have been updated with the above updates, and both the updated servers exhibit the above condition, on the other servers i have no problem accessing root owned file via the editor ?

some more details to this ongoing issue

you really should NOT be booting in "init5" AS root
a lot of distros have already BLOCKED ( disabled )this from being done .
( red hat and Debian still allow it )
if using Gnome as root ,there can be a normal problem CAUSED by logging into gnome AS root when "pam" dose not recognize root in the gui
programs will still ask for the root password but with you already root in the gui ,it will error if root logging into the GUI is blocked .
But this should NOT be the case with you

run Gnome as a normal user
and use the terminal to become root
" su" or " su - "


now the top panel missing ( past posts ) is NOT normal

add that to gnome not recognizing root



however
being root and having the yum gui ASK for the root password
is a normal problem caused by using " the 'pam' hack" to allow root logging into the gui , but you did NOT use that so that is not the cause .

so something " very bad" happened if root is not root any longer



a possible cause but NOT a fix
rhel5 ( and therefor oracle 5 ) is VERY incompatible with A LOT ( most ) third party repos
most WILL want to overwrite critical system files with different rpm's
5 IS VERY susceptible to this

the yum plugin " yum-prioritizes" ( or on a server "protect-base " is better)is needed to stop this from happening ( unless you DO want it to .sometimes this IS wanted )

can you post the output of this
as a normal user run
it is looking like incompatible rpm's are installed

A question where exactly did you get the 3 updates and 2 new packages to install ?

yum repolist
Loaded plugins: security
el5_latest | 1.4 kB 00:00
repo id repo name status
el5_latest Oracle Linux 5Server Latest (x86_64) 10,903
ksplice-uptrack Ksplice Uptrack for OL 37
repolist: 10,940


yum.repos.d]# yum repolist all
Loaded plugins: security
repo id repo name status
el5_addons Enterprise Linux 5Server Add ons (x86_64) disabled
el5_ga_base Oracle Linux 5Server GA installation media cop disabled
el5_latest Oracle Linux 5Server Latest (x86_64) enabled: 10,903
el5_oracle_addons Oracle Software addons for Enterprise Linux 5S disabled
el5_u1_base Enterprise Linux 5Server Update 1 installation disabled
el5_u2_base Enterprise Linux 5Server Update 2 installation disabled
el5_u3_base Enterprise Linux 5Server Update 3 installation disabled
el5_u4_base Enterprise Linux 5Server Update 4 installation disabled
el5_u5_base Enterprise Linux 5Server Update 5 installation disabled
el5_unsupported Productivity Applications for Enterprise Linux disabled
ksplice-uptrack Ksplice Uptrack for OL enabled: 37
ol5_UEK_base Unbreakable Enterprise Kernel for Oracle Linux disabled
ol5_UEK_latest Latest Unbreakable Enterprise Kernel for Oracl disabled
ol5_u5_base Oracle Linux 5Server Update 5 installation med disabled
ol5_u6_base Oracle Linux 5Server Update 6 installation med disabled
ol5_u7_base Oracle Linux 5Server Update 7 installation med disabled
ol5_u8_base Oracle Linux 5Server Update 8 installation med disabled
ol5_u9_base Oracle Linux 5Server Update 9 installation med disabled
repolist: 10,940

the 3 updates came from the uln, the only rpm's i get are from oracle's unbreakable linux network... their package updater uses yum

after installing "KDE", when i connect using the gnome interface as root, their is now a kedit shortcut on the gnome desktop, and i can open
a root file that i can't open with the gnome editor ?..

if i connect to the gnome interface as someone other than root, the top panel shows up, the gnome editor works, but is if su -, and then try to open a root file with the gnome editor i get permission denied.. if i open a terminal session i can use vi to open a root file ?

Now a days normal users have lot of restrictions over them. I think you should better install sudo package (if it's already not available) and add your user account in /etc/sudoers to take root privileges while modifying files not owned by your username and other installation/modifications.

Second, I am quite sure that desktop environment do not make any difference or plays any role in access controls. But anyway, in order to switch to a different desktop env. you can try:

GNOME to KDE:
KDE to GNMOE:
Also you can load KDE while running GNOME as: