Cold nuclear matter effects are those effects which modify the production of charmonia in a nuclear target in the absence of a Quark Gluon Plasma. Understanding them is an essential part of any attempt to interpret charmonium production in heavy-ion collisions. In 2008 the PHENIX experiment recorded data for J/ψ and ψ′ production in sNN=200 GeV d+Au collisions. The J/ψ data span the rapidity range from −2.2 to +2.35 and, taken together with p+A collision data on charmonium modification from lower collision energies, they shed light on the time scale dependence of cold nuclear matter effects on J/ψ production in p(d)+A collisions. The modification of ψ′ production is observed at mid rapidity, and is found to be much stronger than expected from existing models.