how to properly close node-express server?

app.listen() returns http.Server. You should invoke close() on that instance and not on app instance.

Ex.

app.get(
    '/auth/github/callback',
    passport.authenticate('github', { failureRedirect: '/login' }),
    function(req, res) {
        res.redirect('/');

        setTimeout(function () {
            server.close();
            // ^^^^^^^^^^^
        }, 3000)
    }
);

var server = app.listen('http://localhost:5000/');

You can inspect sources: /node_modules/express/lib/application.js

If any error occurs in your express app then you must have to close the server and you can do that like below-

var app = express();
var server = app.listen(process.env.PORT || 5000)

If any error occurs then our application will get a signal named SIGTERM. You can read more SIGTERM here - https://www.gnu.org/software/libc/manual/html_node/Termination-Signals.html

process.on('SIGTERM', () => {
  console.info('SIGTERM signal received.');
  console.log('Closing http server.');
  server.close((err) => {
    console.log('Http server closed.');
    process.exit(err ? 1 : 0);
  });
});

In express v3 they removed this function.

You can still achieve the same by assigning the result of app.listen() function and apply close on it:

var server = app.listen(3000);
server.close((err) => {
  console.log('server closed')
  process.exit(err ? 1 : 0)
})

https://github.com/visionmedia/express/issues/1366