[R-sig-Geo] spatstat crashes R when converting tess to sp objects

[O'Hanlon, Simon J]

Further to this problem, I have experienced some more odd behaviour with the coercion from tess to sp.

My real dataset is 3607 points within the observation window. If I try and run this straight away I get a segfault crash with the error message: 

 *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: .Call("Polygons_c", srl, ID, PACKAGE = "sp")
 2: Polygons(pieces, id)
 3: owin2Polygons(y[[i]], nam[i])
 4: as.SpatialPolygons.tess(from)
 5: asMethod(object)
 6: as(v, "SpatialPolygons")

This is using the spatstat.options(gpclib=T) workaround posted by Roger. However if I take a small sample of say 50 rows from the dataset, run the script on these and coerce from tess to sp it runs fine. Interestingly I can then re-read the data file and run the analysis on all 3607 points within the same R session and corece to sp with no problems at all. However it crashes every time if I don't 'prime' the function with a small run dataset first?!

I can try to provide a reproducible example if that will help more? (the easiest way is if I can share my datapoint locations, but I have to ask permission first). Otherwise I will try to recreate this from within R.

Thanks,

Simon

________________________________________
From: Roger Bivand [Roger.Bivand at nhh.no]
Sent: 28 October 2012 13:43
To: O'Hanlon, Simon J
Cc: Barry Rowlingson; r-sig-geo at r-project.org
Subject: RE: [R-sig-Geo] spatstat crashes R when converting tess to sp objects

On Sun, 28 Oct 2012, O'Hanlon, Simon J wrote:

> Dear Roger and Barry,
> Thank you so much for your, as ever, lightening fast responses. This is
> one of the many reasons why I love using R as a platform so much. That
> workaround has solved the issue for me now.

Simon,

With a good reproducible example available, life is much easier, and in
fact this was a real crash, so sp will be improved (made safer) thanks to
your posting. Making things work better is shared, really, as this case
shows.

Roger

>
> Many, many thanks,
>
> Simon
> ________________________________________
> From: Roger Bivand [Roger.Bivand at nhh.no]
> Sent: 28 October 2012 13:30
> To: Barry Rowlingson
> Cc: O'Hanlon, Simon J; r-sig-geo at r-project.org
> Subject: Re: [R-sig-Geo] spatstat crashes R when converting tess to sp objects
>
> On Sun, 28 Oct 2012, Barry Rowlingson wrote:
>
>> On Sun, Oct 28, 2012 at 12:22 PM, O'Hanlon, Simon J
>> <simon.ohanlon at imperial.ac.uk> wrote:
>>> Dear list,
>>
>>> #Reproducible example
>>
>> I think maptools isn't coping with certain types of tess object. I
>> can reproduce this in three lines without needing a download :)
>
> I'm seeing:
>
> Warning message:
> In as.polygonal(x) :
>   Can't convert mask to polygon: gpclib is disabled/unavailable
>
> called in maptools:::owin2Polygons:
>
> x <- as.polygonal(x)
>
> where x is an element of the list y made from the tesselation in
> maptools:::as.SpatialPolygons.tess by
>
> y <- tiles(x)
>
> Since as.polygonal(x) fails, x$bdry is NULL, and pieces is an empty
> list. I've patched sp:::Polygons() to trap the empty list on R-Forge, so
> that the user will see (using the current status of rspatial/sp on
> R-Forge):
>
>> vp <- as( v , "SpatialPolygons" )
> Error: length(srl) > 0 is not TRUE
> In addition: Warning message:
> In as.polygonal(x) :
>   Can't convert mask to polygon: gpclib is disabled/unavailable
>
> The resolution for now is:
>
> spatstat.options("gpclib"=TRUE)
>
> letting as.polygonal() do its stuff for a W$type "mask" tesselation. Not
> great, but it works; conversion to rgeos from gpclib might also work
> using the wrappers for gpclib objects included in rgeos.
>
> Roger
>
>
>>
>> 1, start R, use some packages:
>>
>> $ R --vanilla
>>
>> R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
>> Copyright (C) 2012 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>> Platform: i486-pc-linux-gnu (32-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>>  Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> library(spatstat)
>> Loading required package: mgcv
>> This is mgcv 1.7-21. For overview type 'help("mgcv-package")'.
>> Loading required package: deldir
>> deldir 0.0-20
>> spatstat 1.28-2
>> Type ‘help(spatstat)’ for an overview of spatstat
>>     ‘latest.news()’ for news on latest version
>>     ‘licence.polygons()’ for licence information on polygon calculations
>>
>> 2. Run this to create some objects:
>>
>>> example(tess)
>>
>> tess>   A <- tess(xgrid=0:4,ygrid=0:4)
>>
>> tess>   A
>> Tessellation
>> Tiles are equal rectangles, of dimension 1 x 1 units
>> 4 by 4 grid of tiles
>> window: rectangle = [0, 4] x [0, 4] units
>>
>> tess>   B <- A[c(1, 2, 5, 7, 9)]
>>
>> tess>   B
>> Tessellation
>> Tessellation is determined by a factor-valued image with 5 levels
>> window: binary image mask
>> 384 x 192 pixel array (ny, nx)
>> enclosing rectangle: [0, 3] x [1, 4] units
>>
>> tess>   v <- as.im(function(x,y){factor(round(5 * (x^2 + y^2)))}, W=owin())
>>
>> tess>   levels(v) <- letters[seq(length(levels(v)))]
>>
>> tess>   E <- tess(image=v)
>>
>> tess>   E
>> Tessellation
>> Tessellation is determined by a factor-valued image with 11 levels
>> window: binary image mask
>> 128 x 128 pixel array (ny, nx)
>> enclosing rectangle: [0, 1] x [0, 1] units
>>
>> 3. Try conversion:
>>
>>> as(E,"SpatialPolygons")
>> Error in as(E, "SpatialPolygons") :
>>  no method or default for coercing "tess" to "SpatialPolygons"
>>
>> 4. Try conversion with maptools:
>>
>>> library(maptools)
>> Loading required package: foreign
>> Loading required package: sp
>> Loading required package: lattice
>> Checking rgeos availability: TRUE
>>> as(E,"SpatialPolygons")
>>
>> *** caught segfault ***
>> address (nil), cause 'memory not mapped'
>>
>> I've not looked at the maptools code, but the tess object can be one
>> of three types according to ?tess, and I bet the conversion code
>> doesn't check what its dealing with...
>>
>> Barry
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
> --
> Roger Bivand
> Department of Economics, NHH Norwegian School of Economics,
> 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

--
Roger Bivand
Department of Economics, NHH Norwegian School of Economics,
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