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We consider the problem of jointly optimizing channel pairing, channel-user assignment, and power allocation, to maximize the weighted sum-rate, in a single-relay cooperative system with multiple channels and multiple users. Common relaying strategies are considered, and transmission power constraints are imposed on both individual transmitters and the aggregate over all transmitters. The joint optimization problem naturally leads to a mixed-integer program. Despite the general expectation that such problems are intractable, we construct an efficient algorithm to find an optimal solution, which incurs computational complexity that is polynomial in the number of channels and the number of users. We further demonstrate through numerical experiments that the jointly optimal solution can significantly improve system performance over its suboptimal alternatives.