Answer by mpettigr for How to prevent flycheck from treating my init.el as a package file?

Here's the format that the checker is actually expecting:

;;; init.el --- Initialization file for Emacs;;; Commentary: Emacs Startup File --- initialization for Emacs

If you place this at the top of your init.el it'll remove the warning.

You can get emacs to insert this for you automatically by going to the menu and selecting Emacs-Lisp->Check Documentation Strings and fill in the requested fields. Source: https://github.com/purcell/emacs.d/issues/152