[R] *** caught segfault *** error

[Juanjo Abellan]

Dear R users,

I use R 2.4.0 on an iMac running Mac OS X 10.4.8, with a 2.16GHz  
Intel Core 2 Duo and 2GB 667 MHz DDR2 SDRAM.

 > sessionInfo()
R version 2.4.0 (2006-10-03)
i386-apple-darwin8.8.1

locale:
es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8

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


I get an error below whenever I try to plot a map from a shapefile  
imported into R; I've tried packages shapefiles and spdep, and two  
different shapefiles, and get the error in all 4 combinations.

The shapefile is imported correctly, and I get the error only when I  
try to plot the map. I specifically use commands

 > library(spdep)
Loading required package: tripack
Loading required package: maptools
Loading required package: foreign
Loading required package: sp
Loading required package: SparseM
Package SparseM (0.71) loaded.  To cite, see citation("SparseM")
Loading required package: boot
 > library(maptools)
 > district.shp <- read.shape("~/Documents/SAHSU/MD/data/Carthography/ 
districts_ok.shp")
Shapefile type: Polygon, (5), # of Shapes: 354
 > plot(district.shp)

*** caught segfault ***
address 0xc00006d5, cause 'memory not mapped'

Traceback:
1: polygon(theMap$Shapes[[ii]]$verts, col = fg[i], border = ol,     ...)
2: plot.Map(district.shp)
3: plot(district.shp)
4: plot(district.shp)

Possible actions:
1: abort (with core dump)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

I saw that plot.Map is deprecated, so I converted the shapefile into  
a polygon list, and then tried to plot it, but still got the error:

 > library(spdep)
Loading required package: tripack
Loading required package: maptools
Loading required package: foreign
Loading required package: sp
Loading required package: SparseM
Package SparseM (0.71) loaded.  To cite, see citation("SparseM")
Loading required package: boot
 > library(maptools)
 > district.shp <- read.shape("~/Documents/SAHSU/MD/data/Carthography/ 
districts_ok.shp")
Shapefile type: Polygon, (5), # of Shapes: 354
 > district.pl <- Map2poly(district.shp, as.character(district.shp$att 
$DISTRICT_2))
 > plot(district.pl)

*** caught segfault ***
address 0xc0000165, cause 'memory not mapped'

Traceback:
1: polygon(coords[pFrom[i]:pTo[i], ], border = border, xpd = xpd,      
density = density, angle = angle)
2: polygonholes(x[[j]], border = border, xpd = xpd, density = density 
[j],     angle = angle[j], pbg = pbg, forcefill = forcefill)
3: plot.polylist(district.pl)
4: plot(district.pl)
5: plot(district.pl)

Possible actions:
1: abort (with core dump)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:


I also get the same error when I use library shapefiles to import the  
shp file and then try to plot the polygons myself; these are the  
commands I run:

 > library(shapefiles)
 > districts.shp <- read.shapefile("~/Documents/SAHSU/MD/data/ 
carthography/districts_ok")

Attaching package: 'foreign'


	The following object(s) are masked from package:shapefiles :

	 read.dbf

	The following object(s) are masked from package:shapefiles :

	 write.dbf

 > ndistricts <- length(districts.shp$shp$shp)
 > keys <- districts.shp$dbf$dbf$DISTRICT_2
 > vertices <- list()
 > for(i in 1:ndistricts){
+ vertices[[i]] <- districts.shp$shp$shp[[i]]$points
+ }
 >
 > districts.map <- list(codigo=keys, vertices=vertices)#,  
nombre=wardnames)
 >
 > xymin <- apply(t(sapply(districts.map$vertices, apply, 2, min)),  
2, min)
 > xymax <- apply(t(sapply(districts.map$vertices, apply, 2, max)),  
2, max)
 > corners <- expand.grid(xymin, xymax)
 >
 > # Plotting the corners and then adding polygons one by one.
 > par(pty="s")
 > plot(rbind(xymin, xymax), type="n")
 > for (i in 1:ndistricts){
+     polygon(x=districts.map$vertices[[i]][,1], y=districts.map 
$vertices[[i]][,2])
+ }

*** caught segfault ***
address 0xc00009d8, cause 'memory not mapped'

Traceback:
1: polygon(x = districts.map$vertices[[i]][, 1], y = districts.map 
$vertices[[i]][,     2])

Possible actions:
1: abort (with core dump)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:


The same commands work fine in my laptop (Intel Pentium 4 CPU 2.00  
GHz, with 512 MB RAM), where I use R v2.2.1 on Windows XP Home  
Edition v2002.

Any ideas of what may cause the error?

Many thanks,

Juanjo Abellan
Research Associate in Statistics
Department of Epidemiology and Public Health
Imperial College London