I'm running the following code to cycle through individual polygons
(surface water basins) in a shapefile and averaging data from a netcdf:

# Extracting basin ID values
basinid<-basin_latlong$value

for (i in basinid) {
  #individual basin extraction
  dummybasin<-basin_latlong[basin_latlong$cat==i,]

  # Extracted basin extent
  dummyextent<-extent(dummybasin)

  # Extract trmm around basin for refinement
    trmm_sub<-crop(trmm,dummyextent,snap="out")

  # Refining resolution by a factor of 10
     trmm_sub<-disaggregate(trmm_sub,fact=10)

  # Rasterizing basin to use as a mask
  mask<-rasterize(dummybasin,trmm_sub)

  # using mask to restrict data to the basin area.
  basintrmm<-mask(trmm_sub,mask=mask)

  # Computing the average timeseries on the basin
  basin_trmm_aveTS<-cellStats(basintrmm,mean)

}

I get the following error:
OGR data source with driver: ESRI Shapefile
Source: "/home/shared/saudi", layer: "Jizan_South_subbasin_poly_clean"
with 42 features and 5 fields
Feature type: wkbPolygon with 2 dimensions
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Found 1 region(s) and 1 polygon(s)
Error in d[, alyrs, drop = FALSE] : incorrect number of dimensions

Basically it works for a while and err on a specific basin with basinids
16, 34, 46,...


thanks

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