Remove calibre. Shut down. Wait 5 seconds or so. Boot up. Run dupeclean (just in case). Check for upgrades. If there are any, do you get the same message? Check for broken packages, too.
Used Zen 32bit for this because it's the traditional, non-testing installation. Started Synaptic. Reload. Mark All Upgrades. Nothing to upgrade. No broken packages before or after. Marked calibre for complete removal. Doing so would have only removed that one package. I've left it installed for now. Ran dupecleangui.
edit: Transaction set lock messages are about the package lists. Run bleachbit-root or manually delete the pkglist files at /var/lib/apt/lists and the 2 pkgcache files at /var/cache/apt before you open and reload synaptic. Do not delete the folders! You need them.
After running bleachbit-user, bleachbit-root and dupecleangui, there were still package list files in the /var/lib/apt/lists directory, as well as a lock file. I deleted them, as well as the two .bin files in the /var/cache/apt directory. Now, I have:
[root@localhost ~]#ls -l /var/lib/apt/lists/
drwxr-xr-x 2 root root 4096 Apr 27 01:09 partial/
[root@localhost ~]#ls -l /var/cache/apt/
drwxr-xr-x 3 root root 16384 Apr 26 14:35 archives/
drwxr-xr-x 2 root root 4096 Jul 19 2011 genpkglist/
drwxr-xr-x 2 root root 4096 Jun 10 2011 gensrclist/
Do you have any pinned packages?
[root@localhost ~]#cat /etc/apt/preferences
I'll post again when there are some packages to be updated.
EDIT: Removed calibre for post in another thread.