Comment 6 for bug 1069350

These directories can indeed be safely removed.

On Ubuntu and other non-rpm-based systems, rpm is typically used to build and inspect RPM packages, not to install them or manage a database. The problem for non-rpm-based systems is that the rpm tool cannot (currently) operate on package files without accessing its database. If the rpmdb doesn't exist, you get a nasty warning (that calls itself an error) with every command:

$ rpm -qp fedora-release-18-0.8.noarch.rpm
error: cannot open Packages database in /var/lib/rpm
fedora-release-18-0.8.noarch

The fix for Debian and Ubuntu was to configure rpm such that it creates a database in $HOME/.rpmdb, since $HOME should normally be writable. See http://bugs.debian.org/551669.

If you want to prevent these directories from being created, you could try to figure out what process is running rpm with HOME set to null or /. I agree with #3, it sounds like cron.

Bottom line, I'm not sure what the bug is here. A lot of Linux commands and applications generate configuration files or directories as a side effect of running, and if you run them as root without a HOME, you'll get the same effect.