Tikz Externalize and Hyperref

Tikz Externalize does not work well with Hyperref without some extra measures. In order to get around the problem, include the following lines in your preamble

\tikzifexternalizing{%
   \newcommand{\hypersetup}[1]{}
}{%
   \usepackage{hyperref}  
}
\hypersetup{
   colorlinks,           % These are of course only example options.
   bookmarksnumbered,
   linkcolor={blue!60!black},
   citecolor={blue!60!black}, 
   urlcolor={blue!60!black}
}

% \hypersetup{draft}    % Remove the comment character for printing. 

Tikzexternalize and Lualatex

In order to use tikzexternalize in lualatex another package is also necessary:

  \usepackage{shellesc} 

Other packages also require {shellesc} with lualatex, and therefore it may seem that it is not necessary sometimes. It is always necessary.