error in readShapePoly

Thanks Roger!

Are there any instances in which one would want delete_null_obj=FALSE?

-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
Sent: Wednesday, June 10, 2009 10:36 AM
To: Hurlbert, Allen H. (Biology)
Subject: RE: [R-sig-Geo] error in readShapePoly

On Wed, 10 Jun 2009, Hurlbert, Allen H. (Biology) wrote:

Hi Roger,

Here is the result of the traceback():

4: .shp2srsI(shapes[[belongs[[i]][j]]],
.nParts.shpI(shapes[[belongs[[i]][j]]]),
      force_ring = force_ring)
3: .asSpatialPolygonsShapes(Map$Shapes, IDs, proj4string =

proj4string,

      force_ring = force_ring)
2: .Map2PolyDF(Map, IDs = IDvar, proj4string = proj4string, force_ring

=

force_ring,
      delete_null_obj = delete_null_obj, retrieve_ABS_null =
retrieve_ABS_null)
1:

readShapePoly(paste("\\\\Bioark.bio.unc.edu\\hurlbertallen\\GIS\\BirdRan

geMaps\\NatureServe3.0\\",
      as.character(families[f]), "\\", as.character(spp.list[s2,
          1]), sep = ""), proj4string = CRS("+proj=latlong
+datum=NAD83"))

The shapefiles are bird range maps available online from NatureServe
here: http://www.natureserve.org/getData/birdMaps.jsp. The problem

file

is trin_inca_pl.shp which is included in the zipped 'Scolopacidae'

file

on that page.

Unfortunately, I am unfamiliar with the syntax of readOGR() and can't
quite figure out how I'm supposed to use it to read in a shapefile.

It is a bit more revealing:

trin_inca_pl <- readOGR("Scolopacidae", "trin_inca_pl")

Error in ogrInfo(dsn = dsn, layer = layer, input_field_name_encoding =
input_field_name_encoding) :
  NULL geometry found

and suggests using the fix in:

trin_inca_pl <- readShapePoly("Scolopacidae/trin_inca_pl.shp",

+  delete_null_obj=TRUE)
Warning message:
In .Map2PolyDF(Map, IDs = IDvar, proj4string = proj4string, force_ring =

force_ring,  :
  Null objects with the following indices deleted: 134

So the data provider has inserted a NULL geometry into the data - they
shouldn't do it, but it has been seen before. Could you summarise to the

list, please? I'll see if I can add a test in readShapePoly to point
users
to the optional argument.

Roger

Thanks!
Allen

-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
Sent: Wednesday, June 10, 2009 9:38 AM
To: Hurlbert, Allen H. (Biology)
Cc: r-sig-geo at stat.math.ethz.ch
Subject: Re: [R-sig-Geo] error in readShapePoly

On Wed, 10 Jun 2009, Hurlbert, Allen H. (Biology) wrote:

Hello list,



I'm new to GIS in R, so I appreciate any pointers with my problem.



I have code that uses readShapePoly to read in shapefiles in a loop

and

does some basic operations. This code appeared to be working great

for

twenty or so files, but then on one shapefile bonked with the

following

error:   Error in from[j]:to[j] : NA/NaN argument.



The problem shapefile opens fine in ArcGIS and there is nothing

readily

different about its attribute table or source information that I can

see

(and furthermore, all shapefiles are from the same standardized

source,

although of course that doesn't mean one of them didn't get messed up
somewhere along the way). I am running 2.7.2 on Windows XP x64.

Could you 1) try readOGR() in rgdal instead of readShapePoly() in
maptools
if possible, and see if the problem is repeated; 2) post either the
output
of traceback() run immediately after the error occurs (will show

where,

more or less, the problem is in code) here and/or the shapefile(s) all
3-4
files in a zip archive on a website and post the URL here so that

others

can debug this? The problem seems to be a shot Pstart vector putting

an

invalid value into the range from which to extract ring coordinates,

but

the question is why it is shot.

If you can say something about the origin of the file, this may also
help
(what software wrote it), some have broken *.shx files.

Roger

Thanks in advance,

Allen


	[[alternative HTML version deleted]]

Thanks Roger!

Are there any instances in which one would want delete_null_obj=FALSE?

-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
Sent: Wednesday, June 10, 2009 10:36 AM
To: Hurlbert, Allen H. (Biology)
Subject: RE: [R-sig-Geo] error in readShapePoly

On Wed, 10 Jun 2009, Hurlbert, Allen H. (Biology) wrote:

Hi Roger,

Here is the result of the traceback():

4: .shp2srsI(shapes[[belongs[[i]][j]]],
.nParts.shpI(shapes[[belongs[[i]][j]]]),
      force_ring = force_ring)
3: .asSpatialPolygonsShapes(Map$Shapes, IDs, proj4string =

proj4string,

      force_ring = force_ring)
2: .Map2PolyDF(Map, IDs = IDvar, proj4string = proj4string,

=

force_ring,
      delete_null_obj = delete_null_obj, retrieve_ABS_null =
retrieve_ABS_null)
1:

geMaps\\NatureServe3.0\\",
      as.character(families[f]), "\\", as.character(spp.list[s2,
          1]), sep = ""), proj4string = CRS("+proj=latlong
+datum=NAD83"))

The shapefiles are bird range maps available online from NatureServe
here: http://www.natureserve.org/getData/birdMaps.jsp. The problem

file

is trin_inca_pl.shp which is included in the zipped 'Scolopacidae'

file

on that page.

Unfortunately, I am unfamiliar with the syntax of readOGR() and can't
quite figure out how I'm supposed to use it to read in a shapefile.

It is a bit more revealing:

trin_inca_pl <- readOGR("Scolopacidae", "trin_inca_pl")

Error in ogrInfo(dsn = dsn, layer = layer, input_field_name_encoding =
input_field_name_encoding) :
  NULL geometry found

and suggests using the fix in:

trin_inca_pl <- readShapePoly("Scolopacidae/trin_inca_pl.shp",

+  delete_null_obj=TRUE)
Warning message:
In .Map2PolyDF(Map, IDs = IDvar, proj4string = proj4string, force_ring

force_ring,  :
  Null objects with the following indices deleted: 134

So the data provider has inserted a NULL geometry into the data - they
shouldn't do it, but it has been seen before. Could you summarise to

list, please? I'll see if I can add a test in readShapePoly to point
users
to the optional argument.

Roger

Thanks!
Allen

-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
Sent: Wednesday, June 10, 2009 9:38 AM
To: Hurlbert, Allen H. (Biology)
Cc: r-sig-geo at stat.math.ethz.ch
Subject: Re: [R-sig-Geo] error in readShapePoly

On Wed, 10 Jun 2009, Hurlbert, Allen H. (Biology) wrote:

Hello list,



I'm new to GIS in R, so I appreciate any pointers with my problem.



I have code that uses readShapePoly to read in shapefiles in a loop

and

does some basic operations. This code appeared to be working great

for

twenty or so files, but then on one shapefile bonked with the

following

error:   Error in from[j]:to[j] : NA/NaN argument.



The problem shapefile opens fine in ArcGIS and there is nothing

readily

different about its attribute table or source information that I can

see

(and furthermore, all shapefiles are from the same standardized

source,

although of course that doesn't mean one of them didn't get messed

somewhere along the way). I am running 2.7.2 on Windows XP x64.

Could you 1) try readOGR() in rgdal instead of readShapePoly() in
maptools
if possible, and see if the problem is repeated; 2) post either the
output
of traceback() run immediately after the error occurs (will show

where,

more or less, the problem is in code) here and/or the shapefile(s)

3-4
files in a zip archive on a website and post the URL here so that

others

can debug this? The problem seems to be a shot Pstart vector putting

an

invalid value into the range from which to extract ring coordinates,

but

the question is why it is shot.

If you can say something about the origin of the file, this may also
help
(what software wrote it), some have broken *.shx files.

Roger

Thanks in advance,

Allen


	[[alternative HTML version deleted]]

Is there an equivalent argument in readOGR() to read in a shapefile with
a NULL geometry, or can this only be done with readShapePoly?

Thanks,
Allen

-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
Sent: Wednesday, June 10, 2009 12:44 PM
To: Hurlbert, Allen H. (Biology)
Cc: r-sig-geo at stat.math.ethz.ch
Subject: RE: [R-sig-Geo] error in readShapePoly

On Wed, 10 Jun 2009, Hurlbert, Allen H. (Biology) wrote:

Thanks Roger!

Are there any instances in which one would want delete_null_obj=FALSE?

Well, they shouldn't be there, really. When I release maptools, with
default delete_null_obj=FALSE, it will report which one, and then:

library(foreign)
tip <- read.dbf("trin_inca_pl.dbf")
tip[134,]

would show the contents of the DBF for the offending NULL geometry.
Setting it to TRUE by default wouldn't warn the user that there was
anything untoward. In this case, the file originator might want to know
that a geometry has gone away, perhaps. In an earlier case, Statistics
Australia was squirrelling data with no spatial position away in a NULL
geometry, which is OK for the DBF, but not OK if the files are (as they
are) intended to contain geometries with attributes.

Roger

-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
Sent: Wednesday, June 10, 2009 10:36 AM
To: Hurlbert, Allen H. (Biology)
Subject: RE: [R-sig-Geo] error in readShapePoly

On Wed, 10 Jun 2009, Hurlbert, Allen H. (Biology) wrote:

Hi Roger,

Here is the result of the traceback():

4: .shp2srsI(shapes[[belongs[[i]][j]]],
.nParts.shpI(shapes[[belongs[[i]][j]]]),
      force_ring = force_ring)
3: .asSpatialPolygonsShapes(Map$Shapes, IDs, proj4string =

proj4string,

      force_ring = force_ring)
2: .Map2PolyDF(Map, IDs = IDvar, proj4string = proj4string,

force_ring

=

force_ring,
      delete_null_obj = delete_null_obj, retrieve_ABS_null =
retrieve_ABS_null)
1:

readShapePoly(paste("\\\\Bioark.bio.unc.edu\\hurlbertallen\\GIS\\BirdRan

geMaps\\NatureServe3.0\\",
      as.character(families[f]), "\\", as.character(spp.list[s2,
          1]), sep = ""), proj4string = CRS("+proj=latlong
+datum=NAD83"))

The shapefiles are bird range maps available online from NatureServe
here: http://www.natureserve.org/getData/birdMaps.jsp. The problem

file

is trin_inca_pl.shp which is included in the zipped 'Scolopacidae'

file

on that page.

Unfortunately, I am unfamiliar with the syntax of readOGR() and can't
quite figure out how I'm supposed to use it to read in a shapefile.

It is a bit more revealing:

trin_inca_pl <- readOGR("Scolopacidae", "trin_inca_pl")

Error in ogrInfo(dsn = dsn, layer = layer, input_field_name_encoding =
input_field_name_encoding) :
  NULL geometry found

and suggests using the fix in:

trin_inca_pl <- readShapePoly("Scolopacidae/trin_inca_pl.shp",

+  delete_null_obj=TRUE)
Warning message:
In .Map2PolyDF(Map, IDs = IDvar, proj4string = proj4string, force_ring

=

force_ring,  :
  Null objects with the following indices deleted: 134

So the data provider has inserted a NULL geometry into the data - they
shouldn't do it, but it has been seen before. Could you summarise to

the

list, please? I'll see if I can add a test in readShapePoly to point
users
to the optional argument.

Roger

Thanks!
Allen

-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
Sent: Wednesday, June 10, 2009 9:38 AM
To: Hurlbert, Allen H. (Biology)
Cc: r-sig-geo at stat.math.ethz.ch
Subject: Re: [R-sig-Geo] error in readShapePoly

On Wed, 10 Jun 2009, Hurlbert, Allen H. (Biology) wrote:

Hello list,



I'm new to GIS in R, so I appreciate any pointers with my problem.



I have code that uses readShapePoly to read in shapefiles in a loop

and

does some basic operations. This code appeared to be working great

for

twenty or so files, but then on one shapefile bonked with the

following

error:   Error in from[j]:to[j] : NA/NaN argument.



The problem shapefile opens fine in ArcGIS and there is nothing

readily

different about its attribute table or source information that I can

see

(and furthermore, all shapefiles are from the same standardized

source,

although of course that doesn't mean one of them didn't get messed

up

somewhere along the way). I am running 2.7.2 on Windows XP x64.

Could you 1) try readOGR() in rgdal instead of readShapePoly() in
maptools
if possible, and see if the problem is repeated; 2) post either the
output
of traceback() run immediately after the error occurs (will show

where,

more or less, the problem is in code) here and/or the shapefile(s)

all

3-4
files in a zip archive on a website and post the URL here so that

others

can debug this? The problem seems to be a shot Pstart vector putting

an

invalid value into the range from which to extract ring coordinates,

but

the question is why it is shot.

If you can say something about the origin of the file, this may also
help
(what software wrote it), some have broken *.shx files.

Roger

Thanks in advance,

Allen


	[[alternative HTML version deleted]]