cld<- raster("cdl_30m_r_il_2014_albers.tif") #this is the large raster
r<- stack(paste(path,"/data_robin/", fl,sep="")) #1 stack,I have 4000 similar
mat<-as.data.frame(getValues(r)) # getting values from the stack
xy<-xyFromCell(r,c(1:ncell(r)),spatial = TRUE)
clip1 <- crop(cld, extent(r)) # Tried to crop it to a smaller size
cells<-cellFromXY(clip1,xy)
mat$landuse<- NA
# mat$landuse<-cld[cells]
mat$landuse<- extract(clip1,cells) #this line takes 5 mins based on profiling

> cld
class       : RasterLayer
dimensions  : 20862, 11758, 245295396  (nrow, ncol, ncell)
resolution  : 30, 30  (x, y)
extent      : 378585, 731325, 1569045, 2194905  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96 +x_0=0 +y_0=0 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0
data source : /Users/kaswani/R/Image/cdl_30m_r_il_2014_albers.tif
names       : cdl_30m_r_il_2014_albers
values      : 0, 255  (min, max)

> r
class       : RasterStack
dimensions  : 9230, 7502, 69243460, 4  (nrow, ncol, ncell, nlayers)
resolution  : 0.7995722, 0.7995722  (x, y)
extent      : 589084.4, 595082.8, 1564504, 1571884  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs
names       : m_3608906_ne_16.1, m_3608906_ne_16.2, m_3608906_ne_16.3, m_3608906_ne_16.4
min values  :                 0,                 0,                 0,                 0
max values  :               255,               255,               255,               255