Do you have an example of what you've tried that doesn't work?
The bootstrapDep in my example would work in the hello sample app in similar fashion, placed somewhere in the static UI. To confirm it's working, you can open your browser's developer tools and inspect network requests or look at the page source. For the example I posted, this is the generated HTML:
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<script type="application/shiny-singletons"></script>
<script type="application/html-dependencies">json2[2014.02.04];jquery[1.12.4];shiny[1.0.5];bootstrap[3.3.7]</script>
<script src="shared/json2-min.js"></script>
<script src="shared/jquery.min.js"></script>
<link href="shared/shiny.css" rel="stylesheet" />
<script src="shared/shiny.min.js"></script>
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" />
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
</head>
<body>
<div class="container-fluid">
<button id="btn" type="button" class="btn btn-default action-button">btn</button>
</div>
</body>
</html>
Without bootstrapDep, it looks like
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<script type="application/shiny-singletons"></script>
<script type="application/html-dependencies">json2[2014.02.04];jquery[1.12.4];shiny[1.0.5];bootstrap[3.3.7]</script>
<script src="shared/json2-min.js"></script>
<script src="shared/jquery.min.js"></script>
<link href="shared/shiny.css" rel="stylesheet" />
<script src="shared/shiny.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="shared/bootstrap/css/bootstrap.min.css" rel="stylesheet" />
<script src="shared/bootstrap/js/bootstrap.min.js"></script>
<script src="shared/bootstrap/shim/html5shiv.min.js"></script>
<script src="shared/bootstrap/shim/respond.min.js"></script>
</head>
<body>
<div class="container-fluid">
<button id="btn" type="button" class="btn btn-default action-button">btn</button>
</div>
</body>
</html>
I just noticed Shiny also includes html5shiv and respond.js with Bootstrap, for legacy browser support (IE 9 and below?). You may want to add these too.