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A general description is here.
The MSI installer is now made by an R script, and there is now support for 64-bit builds. (Unlike the Inno Setup installer, there are separate MSI installers for 32- and 64-bit Windows.)
It is now built using ‘WiX 3.x’ rather than ‘WiX 2.0’. (As a result it is about 25% smaller.)
‘Sweave()’ with ‘keep.source=TRUE’ dropped comments at the start and end of code chunks. It could also fail when ‘\SweaveInput’ was combined with named chunks.