This could happen when using a virtual machine and synced folders, with Linux guest and Windows host. Stack trace might look similar to [bash] npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "install" npm ERR! node v5.10.1 npm ERR! npm v3.8.3 npm ERR! path ../express/bin/express npm ERR! code EPROTO npm ERR! errno -71 npm ERR! syscall symlink

npm ERR! EPROTO: protocol error, symlink ‘../express/bin/express’ -> ‘/vagrant/courselooper/node_modules/.bin/express’ [/bash]

So Windows and POSIX systems have different definitions and implementations for symlink or shortcut. To resolve this, add --no-bin-links flag to npm:

npm install --no-bin-links