Why does my output say "Attempt to index nil with "Position"?

The humanoid is in the character not the player, to access the character use:

player.Character

Then, once you have that, you need to change .magnitude to .Magnitude , i am not sure if that changes anything but i would suggest doing it. Also, use the HRP's position as it is more reliable. Fixed code:

local Player = game.Players.LocalPlayer
local Character = Player.Character -- Character is the character
local hum = Character:FindFirstChild("Humanoid") -- hum is the humanoid
local HRP = Character.HumanoidRootPart -- HRP is the humanoidrootpart
local RunService = game:GetService("RunService") 
local UIS = game:GetService("UserInputService")

local Door = game.Workspace.DualDoorsE.SecondaryDoorE2
local DoorPrimaryPart = Door.PrimaryDoorPart

local NearDoor = false

RunService.RenderStepped:Connect(function()
    if (HRP.Position - DoorPrimaryPart.Position).Magnitude < 5 then -- HRP instead of Player or Character
        NearDoor = true
        DoorPrimaryPart.EToOpen.Enabled = true
    else
        NearDoor = false
        DoorPrimaryPart.EToOpen.Enabled = false
    end
end)

UIS.InputBegan:Connect(function(Input)
    if Input.UserInputType == Enum.UserInputType.Keyboard then
        local Key = Input.KeyCode
        if Key == Enum.KeyCode.E and NearDoor == true then
            Door.ToggleDoor:FireServer()
        end
    end
end)