Um how? – Headers already sent issue

So I was testing my framework (which will blow the minds of WordPress) and I got this issue which I find so weird.

<b>Warning</b>: Cannot modify header information – headers already sent by (output started at /home/adrienk/public_html/wp-content/themes/Aisis/custom/custom-functions.php:3) in <b>/home/adrienk/public_html/wp-includes/functions.php</b> on line <b>862</b>

(it throws the same error for 861 of the same file)

which in this functions file that its spazzing out about is:

setcookie( 'wp-settings-' . $user->ID, $settings, time() + 31536000, SITECOOKIEPATH );
	setcookie( 'wp-settings-time-' . $user->ID, time(), time() + 31536000, SITECOOKIEPATH );

Whats in my custom-functions.php file?

<?php
/*
 * This is your custom functions.php file. Edit it
 * to your hearts content.
 */
?>

so like……wtf?