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Since version 1.1, the execute button in the Compare Basket pane hasn't worked. I add two IBM Core dump histograms to the compare basket and try to click the red exclamation point (tooltip of "Compare the results"), but nothing happens. The last version I've tried is 1.1.0.201107201117. I'm using the IBM build with the DTFJ built in.
Looks like it works using regular Eclipse MAT 1.1 + manual install of the DTFJ, so it must be a problem caused by the IBM build.