Q: duplicity works fine when run standalone, but complains about gpg "public key not found" when run from backupninja A: We bet you're using sudo to run both duplicity and backupninja, and have been using sudo as well when generating the GnuPG key pair used by duplicity. Quick fix: generate a new GnuPG key pair in a root shell, or using "sudo -H" instead of plain sudo. Another solution: import the GnuPG keypair into the root user's keyring, taking care of running "gpg --update-trustdb" in a root shell or using "sudo -H" afterwards, in order to tag this keypair as "ultimately trusted". Detailed explanation: sudo does not change $HOME by default, so GnuPG saved the newly generated key pair to your own keyring, rather than to the root user's keyring. Running "sudo duplicity" hides the problem, as it uses your own keyring. Running "sudo backupninja" reveals the problem, as backupninja uses "su" to make sure it runs duplicity in a real root environment, i.e. using the root user's GnuPG keyring.