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Yubikeys are closed hardware smart cards capable of providing one time passwords, hardware encryption, and storing OpenPGP keys. Many connect to workstations over a USB interface.
There are a few packages that may be helpful in using and managing a Yubikey.
emerge --ask app-crypt/ccid
emerge --ask sys-apps/pcsc-lite
Systems running on systemd can troubleshoot the pcscd daemon with journalctl:
journalctl -u pcscd.service