Gnome Keyring hijacks the connection to GPG Agent (effectively performing a man-in-the-middle attack)
by setting the GPG_AGENT_INFO environment variable to point to itself.  It then filters all communication
with gpg-agent.  gpg detects this and issues the following warning:

{{{
gpg: WARNING: The GNOME keyring manager hijacked the GnuPG agent.
gpg: WARNING: GnuPG will not work properly - please configure that tool to not interfere with the GnuPG system!
}}}

You can read more about the issue [[https://lists.gnupg.org/pipermail/gnupg-devel/2014-August/028689.html|here]]
according to both the GnuPG developpers and the Gnome Keyring developers.  The motivation for hijacking the
connection is that Gnome Keyring wants to:

  # provide a pretty dialog for requesting the user's password
  # save the user's pass phrase in Gnome Keyring so that the user doesn't need to enter the pass phrase.

Unfortunately, Gnome Keyring's implementation of the protocol is incomplete.  Thus although many operations work,
in particular, working with smart cards results in errors that look like this:

{{{
$ echo | gpg2 --sign
gpg: WARNING: The GNOME keyring manager hijacked the GnuPG agent.
gpg: WARNING: GnuPG will not work properly - please configure that tool to not interfere with the GnuPG system!
gpg: selecting openpgp failed: Unsupported certificate
gpg: signing failed: Unsupported certificate
}}}

For one way to work around this issue, see [[http://blog.josefsson.org/2015/01/02/openpgp-smartcards-and-gnome/|this blog by Simon Josefsson]].