[R-sig-Geo] Issues importing BIG shapefile - Limitations of R or something else?

[Roger Bivand]

On Sat, 28 Mar 2009, Tyler Dean Rudolph wrote:

> Here are the sessionInfo() and traceback() results following the failed
> import.  It looks like I am not using the most recent version of sp so I am
> trying to figure out the terms in the call to update.package() and with the
> most recent version I will try again.

Thanks! The indications are that coordinates is being passed a numeric 
vector, not a matrix, at:

Line(coords = shape$verts[from[i]:to[i], ])

so if from[i] == to[i], the code as shown converts a single coordinate 
(one row) matrix into a numeric vector (omitted drop=FALSE in "[" method, 
perhaps the most common coding error in S/R).

That is fixable, but a better workaround may be to use readOGR() in rgdal 
rather than readShapeLines() in maptools.

Roger

> The .shp file is ~30 megabytes and
> the associated .dbf is ~15 megabytes, though I don't think the latter is
> included in the import.  I have 2G of memory on this machine....
>
> Tyler
>
> **
> *> roads<-as(as(readShapeLines(fn="D:\\GIS\\road2004.shp"), "SpatialLines"),
> "psp")
> *Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "coordinates", for
> signature "numeric"
>
> *> sessionInfo()*
> R version 2.8.1 (2008-12-22)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_MONETARY=English_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] spatstat_1.15-0 deldir_0.0-7    gpclib_1.4-3    mgcv_1.4-1.1
> maptools_0.7-20 foreign_0.8-29  sp_0.9-29
> loaded via a namespace (and not attached):
> [1] grid_2.8.1      lattice_0.17-17 tools_2.8.1
>
> *> traceback()*
> 13: stop("unable to find an inherited method for function \"", fdef at generic,
>
>        "\", for signature ", cnames)
> 12: function (classes, fdef, mtable)
>    {
>        methods <- .findInheritedMethods(classes, fdef, mtable)
>        if (length(methods) == 1)
>            return(methods[[1]])
>        else if (length(methods) == 0) {
>            cnames <- paste("\"", sapply(classes, as.character),
>                "\"", sep = "", collapse = ", ")
>            stop("unable to find an inherited method for function \"",
>                fdef at generic, "\", for signature ", cnames)
>        }
>        else stop("Internal error in finding inherited methods; didn't
> return a unique method")
>    }(list("numeric"), function (obj)
>    standardGeneric("coordinates"), <environment>)
> 11: coordinates(coords)
> 10: Line(coords = shape$verts[from[i]:to[i], ])
> 9: .shapes2LinesList(shapes[[i]], ID = IDs[i])
> 8: .shp2LinesDF(Map, proj4string = proj4string)
> 7: withCallingHandlers(expr, warning = function(w)
> invokeRestart("muffleWarning"))
> 6: suppressWarnings(.shp2LinesDF(Map, proj4string = proj4string))
> 5: readShapeLines(fn = "D:\\GIS\\road2004.shp")
> 4: .class1(object)
> 3: as(readShapeLines(fn = "D:\\GIS\\road2004.shp"), "SpatialLines")
> 2: .class1(object)
> 1: as(as(readShapeLines(fn = "D:\\GIS\\road2004.shp"), "SpatialLines"),
>       "psp")
>
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-- 
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