*** caught segfault *** error

On Thu, 30 Nov 2006, Roger Bivand wrote:

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)

And also please run sessionInfo() *after* attaching the packages,  
since all the version information on those packages is missing in  
the log you sent.

It is possibly a locale issue (non-UTF-8 strings in the  
shapefile?), so you might like to try this in the C locale.

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

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595