(from the README)
(1) Run the script gaze_procs_Step1-hv2_cc. This produces two image files and the plots to check the calibration.
(2) Run gaze_procs_Step2-hv2_cc to execute the statistical analyses for looking time.
(3) Run pupil_procs_Step1-hv2_cc. This produces one image file with the processed pupil dilation data.
(4) Run pupil_procs_Step2-hv2_cc to execute the statistical analyses for pupil dilation. Not that this uses output from (1) and (2).
Make sure that you always load the most recent R-images at steps (2) and (4).