"Object [ null ] has no method 'createWindow' d3"In jsdom's changelog it was mentioned that jsdom.createWindow was among removed jsdom APIs in version 1.0.0-pre.1. BTW, latest version of jsdom as of this writing is 1.0.0-pre.6, so a default installation of jsdom via "npm install jsdom" will not contain support for createWindow.
Hence, it seems that to run d3.js, older jsdom must be used, i.e., version 0.11.1 which is the latest version before 1.0.0-pre.1:
sudo npm remove jsdom
sudo npm install jsdom@0.11.1