[R-sig-Geo] Slow writing of point features to SpatialLite-DB or Geopackage

[manuel.schneider at agroscope.admin.ch]

Dear list

I am searching alternatives to ESRI shapefiles for the storage of GPS data, i.e. tagged point features, and came across SpatialLite or Geopackage. Unfortunately writing to both formats is very slow compared to shapefiles making practical use impossible.

library(sf)
library(rgdal)
library(RSQLite)

n<- 1000
d <-data.frame(a=1:n, X=rnorm(n,1,1), Y=rnorm(n,1,1))
mp1 <- st_as_sf(d, coords=c("X","Y"))

t1 <- system.time(st_write(mp1, dsn = 'C:/Temp/data1.shp', driver = 'ESRI Shapefile'))
t2 <- system.time(st_write(mp1, dsn = 'C:/Temp/test.sqlite', layer = 'data1', driver = 'SQLite'))
t3 <- system.time(st_write(mp1, "C:/Temp/data1.gpkg"))

rbind(t1,t2,t3)[,1:3]

   user.self sys.self elapsed
t1      0.03     0.03    0.09
t2      0.53     5.04   29.33
t3      0.48     4.29   32.19

As n increases, processing time explodes for SpatialLite and Geopackage, and I usually have a couple of 10000 points to store. Any experiences of others would be highly appreciated.
Many thanks
Manuel


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R version 3.4.1 (2017-06-30)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=German_Switzerland.1252  LC_CTYPE=German_Switzerland.1252   
[3] LC_MONETARY=German_Switzerland.1252 LC_NUMERIC=C                       
[5] LC_TIME=German_Switzerland.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] sf_0.5-3    RSQLite_2.0 rgdal_1.2-8 sp_1.2-5   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12    lattice_0.20-35 digest_0.6.12   grid_3.4.1      DBI_0.7        
 [6] magrittr_1.5    units_0.4-5     rlang_0.1.2     blob_1.1.0      tools_3.4.1    
[11] udunits2_0.13   bit64_0.9-7     bit_1.1-12      compiler_3.4.1  memoise_1.1.0  
[16] tibble_1.3.4