the key problem here is that the SpatialPoints() takes lon&lat (i.e. x-y) as default, but you gave it lat&lon, which might generate a wrong coordinate (switched x & y ). so nothing is going to be extracted.
> lonlat <- expand_grid(
+ x = sample(seq(4,55,.5),100,replace = T),
+ y = sample(seq(60,150,.5),100,replace = T),
+ )
> SpatialPoints(lonlat %>% select(x,y))
class : SpatialPoints
features : 10000
extent : 4.5, 54.5, 61.5, 149.5 (xmin, xmax, ymin, ymax)
crs : NA
> SpatialPoints(lonlat %>% select(y,x))
class : SpatialPoints
features : 10000
extent : 61.5, 149.5, 4.5, 54.5 (xmin, xmax, ymin, ymax)
crs : NA
so you'll need to correct the coords of SpatialPoints that are used to extract data.