Preheat oven to 350 F. Grease a 9x13 baking dish. Sprinkle the coconut flakes in an even layer in the baking dish. Top with the chopped pecans.
Prepare the chocolate cake according to package directions and pour over the coconut flakes and pecans. Spread evenly.
Beat cream cheese, sugar, butter and vanilla until smooth. Drop dollops of this mixture on the surface of the cake batter, spacing them evenly. Use a knife and swirl it across the batter two or three times to create the swirled/ marbled effect. Sprinkle the chocolate chunks on top. Bake cake at 350 F for 45-50 minutes until cake is just set.