library(raster)
library(sp)

# create rasters and store them in a list
r1 <- raster(xmn=1, xmx=5, ymn=1, ymx=5, nrows=4, ncols=4)
r1[] <- 1:length(r1)

# create SpatialPolygonsDataFrame
Sr1 = Polygon(cbind(c(1,5,4,1,1),c(1,2,5,4,1)))
Sr2 = Polygon(cbind(c(2,4,3,2),c(3,2,4,3)))
SpP = SpatialPolygons(list(Polygons(list(Sr1), "s1"), Polygons(list(Sr2), "s2")),
                      1:2)
dat = data.frame(ID = c("s1", "s2"), value = c("a", "b"))
row.names(dat) <- c("s1", "s2")
p <- SpatialPolygonsDataFrame(SpP, data = dat,
                              match.ID = TRUE)

AddHoleToPolygon <-function(poly,hole){
  # invert the coordinates for Polygons to flag it as a hole
  coordsHole <-  hole@polygons[[1]]@Polygons[[1]]@coords
  newHole <- Polygon(coordsHole,hole=TRUE)

  # punch the hole in the main poly
  listPol <- poly@polygons[[1]]@Polygons
  listPol[[length(listPol)+1]] <- newHole
  punch <- Polygons(listPol,poly@polygons[[1]]@ID)

  # make the polygon a SpatialPolygonsDataFrame as the entry
  new <- SpatialPolygons(list(punch),proj4string=poly@proj4string)
  new <- SpatialPolygonsDataFrame(new,data=as(poly,"data.frame"))

  return(new)
}

punchedPoly <-AddHoleToPolygon(p[1,],p[2,])

p1 <- rbind(p, punchedPoly, makeUniqueIDs = TRUE)
p1 <- p1[2:3,]

masked_hole <- mask(r1, p1)
plot(masked_hole)

m3 <- mask(r1, p1[c(2,1),])
plot(m3)

r2 <- rasterize(p1, r1, field = "value")
plot(r2)
r3 <- rasterize(p1[c(2,1),], r1, field = "value")
plot(r3)