library(raster)
library(sp)

r <- raster(xmn=1, xmx=5, ymn=1, ymx=5, nrows=4, ncols=4)
r[] <- 1:length(r)

Sr1 = Polygon(cbind(c(2,4,4,1,2),c(2,3,5,4,2)))
Sr2 = Polygon(cbind(c(4.1,4,2),c(2,3,2)))

SpP = SpatialPolygons(list(Polygons(list(Sr1), "s1"), Polygons(list(Sr2), "s2")), 1:2)

plot(mask(r, SpP))
plot(SpP,  add=TRUE)