The user is notified of the required permissions when they want to install it from the Android Market. Users cannot choose, allow or deny a permission; they are notified of the permissions that the applications require, and by choosing to install the application, they accept that the required permissions will be granted.
If the new version of your application were to add new permissions, this would be a manual update, and the user would have to accept new permissions to upgrade to the new version.
But users cannot selectively deny software permissions during installation; this is not how permissions for android work.
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