library(sp)
library(raster)

# Create Raster
r <- raster(ncol=40, nrow=20)
r[] <- rnorm(n=ncell(r))

# Create Polygon
a <- seq(-150,150,1)
b <- 50*a^2/(150^2)
df <- data.frame(a=a,b=b)
srl <- Polygon(df, hole=as.logical(NA))
Srl <- Polygons(list(srl), 1)
poly <- SpatialPolygons(list(Srl), pO = 1:length(Srl), proj4string=CRS(as.character(NA)))

# Plot raster and polygon
plot(r)
plot(poly, add=T)

# Mask and plot
rr <- mask(r, poly)
plot(rr)

# The previous code snippet must be executed prior to this one
e1 <- c(-180,180,180,-180)
e2 <- c(90,90,-90,-90)
df2 <- data.frame(e1=e1,e2=e2)
srl2 <- Polygon(df2, hole=F)
Srl2 <- Polygons(list(srl2), 2)
poly2 <- SpatialPolygons(list(Srl2))
srl3 <- Polygon(df)
Srl3 <- Polygons(list(srl3), 1)
poly3 <- SpatialPolygons(list(Srl2,Srl3))

hole <- poly
polyX <- poly2
coordsHole <-  hole@polygons[[1]]@Polygons[[1]]@coords
newHole <- Polygon(coordsHole,hole=TRUE)
listPol <- polyX@polygons[[1]]@Polygons
listPol[[length(listPol)+1]] <- newHole
punch <- Polygons(listPol,polyX@polygons[[1]]@ID)
new <- SpatialPolygons(list(punch),proj4string=poly@proj4string)

plot(r)
plot(new, col="white", border="NA", add=T)