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I was having this same issue and fixed it with the following:

  1. I was also running Macports (Homebrew does not like this), so the first step was to move /opt/local to ~/macports "sudo mv /opt/local ~/macports" per the "$ brew doctor" recommendation when it discovered macports config files. My guess is that this is what ultimately fixed the issue, but I also took further steps suggested in the post linked below.
  2. Manually forced generation of dot config file: $ dot -c
  3. Verified the the existence of the folder "/usr/local/lib/graphviz" and the config6 file.