Q:

How to fix a Package Manager Error in notification area after upgrading a fresh install of lucid with a '/home' from Jaunty?

I just installed 10.04, and used manual partitioning to preserve my '/home' from a 9.04 install. (To be clear: I did not upgraded 9.04 to 10.04, but installed 10.04 off a of CD, keeping only my '/home'.) After the sucessful 10.04 install, I used synaptic to apply all updates, rebooted, removed some packages (mostly tomboy and bluetooth), rebooted, and then used synaptic to install tonnes of packages, mostly from lucid/main and lucid-updates/main, though I also did install a number from lucid/universe and lucid-updates/universe.
A minute or so after the mass installation of new packages, a red circular icon with a white bar running horizontally through it appeared in my notification area. (The icon is quite like the "Do not enter this road" sign pictured here.) On hovering my mouse over the icon, I get the following message:

An error occurred, please run Package Manager from the right-click menu or apt-get in a terminal to see what is wrong. The error message was: 'Unknown Error: '' (E:Opening configuration file /etc/apt/apt.conf.d/99synaptic - ifstream::ifstream (13: Permission denied))' This usually means that your installed packages have unmet dependencies

(Since there was no way to copy the text, I transcribed it; it isn't impossible that it is not a completely faithful transcription.)
I then ran the following commands:

sudo apt-get check
sudo apt-get clean
sudo apt-get autoclean
sudo apt-get autoremove

and then ran those same commands (in that order) but also with the -f flag. I then rebooted. This hasn't removed the warning icon from the notification area. So, I am at a loss for how to proceed.
[Snip a lot of detail about what packages I'd installed and removed that turned out not to be relevant at all.]

A:

This should fix the permission problem (from this thread):
sudo chmod o+r /etc/apt/apt.conf.d/99synaptic

But usually if you have broken dependencies you'd look in synaptic, aptitude or fire off:
sudo dpkg --configure -a

