jQuery - "fadeIn is not a function"

The default template for Bootstrap 4 uses th "slim" version of jQuery which doesn't include many functions. You need to switch back to using a more featured version. For example:

body {
  display:none;
}
<!DOCTYPE html>
<html lang="en">
  <head>
    <!-- Required meta tags -->
    <meta charset="utf-8">
    <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">

    <!-- Bootstrap CSS -->
    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-beta/css/bootstrap.min.css" integrity="sha384-/Y6pD6FV/Vv2HJnA6t+vslU6fwYXjCFtcEpHbNJ0lyAFsXTsjBbfaDjzALeQsN6M" crossorigin="anonymous">

    <link rel="stylesheet" href="css/custom.css">
  </head>
  <body>
    Test

    <!-- Optional JavaScript -->
    <!-- jQuery first, then Popper.js, then Bootstrap JS -->
    <script src="https://code.jquery.com/jquery-3.2.1.min.js"></script>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.11.0/umd/popper.min.js" integrity="sha384-b/U6ypiBEHpOf/4+1nzFpr53nxSS+GLCkfwBdFNTxtclqqenISfwAzpKaMNFNmj4" crossorigin="anonymous"></script>
    <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-beta/js/bootstrap.min.js" integrity="sha384-h0AbiXch4ZDo7tp9hKZ4TsHbi047NrKGLO3SEJAg45jXxnGIfYzk4Si90RDIqNm1" crossorigin="anonymous"></script>

    <script type="text/javascript">
      $(document).ready(function(){
        $('body').fadeIn();
      })
    </script>
  </body>
</html>

The slim version is enough with a small CSS:

jQuery("#toTop").addClass('fade-in');

and

.fade-in {
    opacity: 1;
    animation-name: fadeInOpacity;
    animation-iteration-count: 1;
    animation-timing-function: ease-in;
    animation-duration: 0.5s;
}

@keyframes fadeInOpacity {
    0% {
        opacity: 0;
    }
    100% {
        opacity: 1;
    }
}