Ubuntu :: Software Center Items Cannot Be Installed

For some reason (unknown to me) my Ubuntu Software Center will no longer do installs, I keep getting a pop up window with the message:
Items cannot be installed or removed until the package catalog is repaired. Do you want to repair it now?

If I click Repair and then input in my password I get a another pop-up window which says:
Package operation failed
The installation or removal of a software package failed.

The Details say:
installArchives() failed: Preconfiguring packages ...
Preconfiguring packages ...
Preconfiguring packages ...
(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 202950 files and directories currently installed.)
Unpacking sun-java6-jre (from .../sun-java6-jre_6.26-1natty1_all.deb) .....

And then the first pop-up pops up again and the whole process repeats for a while, until I hit cancel enough times that I get another pop-up window which says:
The package system is broken. Check if you are using third party repositories. If so disable them, since they are a common source of problems. Furthermore run the command in a Terminal: apt-get install -f

The details say this:
The following packages have unmet dependencies:
jonas-5.2: Depends: java5-jdk but it is not installed
Depends: upstart-job but it is a virtual package

When I run that command in a terminal I get:
dlazov@ubuntu:~$ apt-get install -f
E: Could not open lock file /var/lib/dpkg/lock - open (13: Permission denied)
E: Unable to lock the administration directory (/var/lib/dpkg/), are you root?

I also tried the following but not sure what exactly it means or how to fix or repair any of this:
dlazov@ubuntu:~$ gsettings set com.canonical.Unity.Panel systray-whitelist "['all']"
dlazov@ubuntu:~$ sudo apt-get install compizconfig-settings-manager
[sudo] password for dlazov:
Reading package lists... Done
Building dependency tree
Reading state information... Done
compizconfig-settings-manager is already the newest version.
You might want to run 'apt-get -f install' to correct these:

The following packages have unmet dependencies:
jonas-5.2 : Depends: sun-java6-jdk but it is not going to be installed or java5-jdk but it is not installable
E: Unmet dependencies. Try 'apt-get -f install' with no packages (or specify a solution).
dlazov@ubuntu:~$

I saw in the error log a command to type in I tried that but got this:
dlazov@ubuntu:~$ dpkg-reconfigure debconf
/usr/sbin/dpkg-reconfigure must be run as root
dlazov@ubuntu:~$
I never created a root user during installation and I have no idea on how to login as root. ?