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Please cook the beans over low heat, taking your time.
Literal
Low-flame [with-で] time [obj-を] apply-[and-て] beans [obj-を] cook [please-てください].
とろ火 'low flame / simmering heat' is a cooking-term compound from とろ (softness) + 火 'fire.' 時間をかける is the set collocation for 'to take time / put time into' something. 炊く is the dedicated cooking verb for rice and beans — boiled until soft — distinct from 煮る 'simmer,' 茹でる 'boil,' 焼く 'grill / bake.' The instrumental で marks とろ火 as the cooking means.