I have a GeoPackage (.gpkg) database with only one layer:

[1] "ay_riks"
[1] "GPKG"
[1] 1

There are too many objects and I'd like to read only a subset of them based on an attribute:

                 layer = "ay_riks",
                 EWKB = T,
                 query= "SELECT * FROM ay_riks WHERE KOMMUNKOD='2480';")

I get an error:

Reading layer `ay_riks' from data source `/Users/chihayakenji/Documents/spatial_r/data/LM_data/zipped/ay_riks.gpkg' using driver `GPKG'
Error in st_sf(x, ..., agr = agr, sf_column_name = sf_column_name) : 
  no simple features geometry column present

What is the correct way of doing this?

  • I would try to read the GeoPackage first with ogrinfo and verify if "no simple features geometry column present" is misleading error.
    – user30184
    Nov 13, 2019 at 16:24
  • There are geometry columns present. If I read the package without a query statement they are there.
    – Kenji
    Nov 13, 2019 at 16:31
  • 1
    Try geometry_column instead of geom_column: docs: st_read(dsn, layer, ..., query = NA, options = NULL, quiet = FALSE, geometry_column = 1L, type = 0, promote_to_multi = TRUE, although you dont need to specify it unless your table has more than one geom column or isn't a proper geometry table...
    – Spacedman
    Nov 13, 2019 at 17:13
  • @Spacedman you were spot on. The following worked: dta<-st_read("data/LM_data/zipped/ay_riks.gpkg", layer = "ay_riks", geometry_column="geom", query= "SELECT * FROM ay_riks WHERE KOMMUNKOD = '2480';")
    – Kenji
    Nov 13, 2019 at 17:29
  • Since this question was essentially due to my lack of attention to the documentation, should I delete it? The answer boils down to "read the documentation carefully."
    – Kenji
    Nov 13, 2019 at 17:32

1 Answer 1


Although this does not explicitly resolve your issue, the following example should demonstrate that the st_read function can be used successfully in conjunction with an SQL query. As mentioned above, the first step is to confirm that the layer within the GeoPackage contains simple feature geometry column:

ogrinfo lut_data.gpkg 
1: lut_data (Multi Polygon)

We can read in the gpkg into R initially without any SQL query to confirm that all features are read:


data <- st_read('lut_data.gpkg', layer='lut_data')

We can confirm that all features have been read in:

[1] 60  3

and plot the output


enter image description here

We can now repeat the above steps, but only import the features where the lut == 'CHF', as follows:

 data <- st_read('lut_data.gpkg', layer='lut_data', \ 
                query='SELECT * FROM lut_data WHERE LUT ="CHF"')

We should now have imported a subset of the features:

[1] 42  3

and we can plot the data to confirm the output (and check for missing features from the above figure). enter image description here

  • +1 for the nice guide for doing it. It turns out I was specifying the geometry column argument wrongly and that led to my error.
    – Kenji
    Nov 13, 2019 at 17:35

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