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See #1410 for an in-depth explanation of the problem and the solution (selection.interrupt added in version 3.3). To summarise, existing transitions need to be interrupted before registering new ones, in particular when the new transition starts before or at the same time as the old one ends.
In other words, in the example above you need to replace:
This Animated Line Graphs example from http://bl.ocks.org/benjchristensen/1148374 works correctly under v2, but doesn't animate under v3.3.9
Are there any radical differences between v2 and v3 that make the above script invalid?
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