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
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
Dear all,
The shapefile was generated with ArcGIS 9.0 running on Windows XP. It
can be can be found in www.uv.es/~abellan/districts_ok.zip.
Re running sessionInfo() before the error occurres as suggested by
Prof. Ripley:
> 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)
> 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"
other attached packages:
spdep boot SparseM maptools sp foreign tripack
"0.3-32" "1.2-26" "0.71" "0.6-3"
"0.9-4" "0.8-17" "1.2-10"
> 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]]$verts, col = fg[i], border = ol, ...)
2: plot.Map(district.shp)
3: plot(district.shp)
4: plot(district.shp)
Possible actions:
1: abort (with core dump)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
Re trying maptools "example(read.shape)" as suggested by Dr Bivand:
> example(read.shape)
rd.shp> x <- read.shape(system.file("shapes/sids.shp", package =
"maptools")[1])
Shapefile type: Polygon, (5), # of Shapes: 100
rd.shp> length(x$Shapes)
[1] 100
rd.shp> unlist(lapply(x$att.data, class))
AREA PERIMETER CNTY_ CNTY_ID NAME FIPS
FIPSNO CRESS_ID BIR74 SID74
"numeric" "numeric" "numeric" "numeric"
"factor" "factor" "numeric"
"numeric" "numeric" "numeric"
NWBIR74 BIR79 SID79 NWBIR79
"numeric" "numeric" "numeric" "numeric"
rd.shp> str(getinfo.shape(system.file("shapes/fylk-val.shp",
package = "maptools")[1]))
List of 5
$ : chr "/Library/Frameworks/R.framework/Versions/2.4/Resources/
library/maptools/shapes/fylk-val.shp"
$ : int 3
$ : int 97
$ : num [1:4] -4868 6456207 0 0
$ : num [1:4] 1084722 7841997 0 0
- attr(*, "class")= chr "shapehead"
> plot(x)
Warning message:
'plot.Map' is deprecated.
Use 'plot.Spatial' instead.
See help("Deprecated") and help("maptools-deprecated").
The maps is plotted.
Sorry, I didn't understand the issue about the locale and the C
locale that Prof Ripley mentioned. Where could I learn about that?
Thanks,
Juanjo
El 30/11/2006, a las 11:41, Prof Brian Ripley escribi?:
> 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
>>>
>>> ______________________________________________
>>> 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.
>>>
>>
>>
>
> --
> 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