Also, as illustrated in commit InsightSoftwareConsortium/ITK@01580b3, the method itk::ProcessObject::SetInput was part of the deprecated API.
Worth noting that while Slicer is built against an ITK having ITKV3_COMPATIBILITY option OFF, the option ITK_LEGACY_REMOVE is still OFF. See here
Anticipating the transition to ITK 5.0, we will look into turning that option ON . This is captured in the following issue: https://issues.slicer.org/view.php?id=4522