This is probably caused by an update of ESS rather than some change in Org, however Org should probably bind ess-ask-for-ess-directory to nil during batch testing at least. There may be other customizations that need to be taken care of, I also get
Cannot read history file […]/org-mode/testing/examples/.Rhistory in the testing output. Someone who actually uses ESS on a regular basis needs to decide the appropriate course. Regards, Achim. -- +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+ SD adaptations for KORG EX-800 and Poly-800MkII V0.9: http://Synth.Stromeko.net/Downloads.html#KorgSDada