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

[Roger Bivand]

On Thu, 30 Nov 2006, Juanjo Abellan wrote:

> 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.
> 

Please make a copy of the offending shapefile available either on a 
website or attach it to me off-list. It would be useful to know its origin 
(which software wrote it) and whether the copy on the iMac is identical to 
the copy on the Windows PC (perhaps attach both?). Can other shapefiles be 
read on the iMac?

(This may be an R-sig-Mac issue as well as an R-sig-geo issue, so if other 
iMac users could check whether example(read.shape) in the maptools package 
works for them on similar hardware, I'd be grateful)

>  > 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
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 

-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no