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We upgraded to rails 2.1 and polonium and our rspecs
are not running on CI, but run fine if you simply use rake on the
command line.

Check to see if you are using the rake extensions in pivotal core bundle.

Using setTimeout() to wait for DOM to update in JsUnit does not work.

Using setTimeout in tests is not going to do what you want, unless you mock setTimeout. Basically, setTimeout kicks off another thread which is not likely to effect the current test.