Heat flour in a large saucepan over medium heat until it turns light brown, stirring constantly. Remove from heat. In a separate pan melt the butter over medium heat and add the onions. Saute the onions until transparent. Stir in the wine and beef stock. Season with salt and pepper to taste. Cook, stirring frequently for 30 minutes. Put a slice of bread into each serving bowl, and sprinkle Gruyere cheese on each slice. Add soup to the bowls and serve immediately.