I just tried the same test on Ubuntu with all the latest packages and had the
same problem.
writeOGR does not work for GeoJSON
cities <- readOGR(system.file("vectors", package = "rgdal")[1], "cities")
is.na(cities$POPULATION) <- cities$POPULATION == -99
summary(cities$POPULATION)
td <- "."
writeOGR(cities, td, "cities", driver="ESRI Shapefile") # this works
writeOGR(cities, td, "cities", driver="GeoJSON") # this fails
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