[R-sig-Geo] rgeos 'union' causes R crash

[Colin Rundel]

Hi Ben,

My best guess based on the information you have provided is that R is running out of memory, particularly for complex polygons Unions can use a huge amount of memory. Can you check with the task manager what the memory usage looks like when running your code?

-Colin

On Sep 7, 2011, at 8:26 AM, Ben Weinstein wrote:

> Hi all-
> 
> I'm having an odd issue with the gUnion family of commands from the rgeos
> package. I'm importing a series of polygons (species) and trying to find the
> centroid. Each species is only allowed one centroids, so i need to union the
> multiple polygons. this code works great when run line by line. But when run
> as an actual loop, but adding the {} at beginning and end, it gives me a
> runtime error. I have debugged it to the level that i know it is the union
> polygon step. I am running R 2.13, and it was designed for 2.13.1, is that
> really making the difference? When run, R completely freezes and windows
> shuts it down.
> 
> library(rgdal)
> library(PBSmapping)
> library(maptools)
> library(raster)
> library(rgeos)
> #Enter File Directory Below
> setwd("D:/Ben/R/Trochilidae")
> #Pull in all shapefiles in that folder that are polygons
> a<-list.files(pattern='pl.shp$', full.names=FALSE)
> output<-matrix(nrow=length(a),ncol=3)
> colnames(output)<-c("Sci_Name","X_centroid","Y_centroid")
> for(x in 1:length(a)){
> output[(x),1]<-paste(gsub(".shp","",a[x]))
> range<-readShapePoly(a[x], delete_null_obj=TRUE)
> subsetx<-range[range$PRESENCE == 1,]
> subsetx2<-subsetx[subsetx$ORIGIN ==1|subsetx$ORIGIN==2,]
> z<-matrix(length(subsetx2),1, data=1)
> Union<-unionSpatialPolygons(subsetx2,z)
> Breeding.ps<- SpatialPolygons2PolySet(Union)
> Breeding.centroids<- calcCentroid(Breeding.ps, rollup=1)
> output[x,2:3]<-as.matrix(Breeding.centroids[2:3])}
> 
> thanks
> 
> ben weinstein
> 
> 
> 
> 
> -- 
> Ben Weinstein
> Graduate Student
> Ecology and Evolution
> Stony Brook University
> 
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