[R-sig-Geo] rgdal 1.1-1 bug?

Sat Dec 5 11:49:49 CET 2015

On Sat, 5 Dec 2015, Tom Philippi wrote:

> James & all--

If you make the offending shapefile available, I'll look at this in a week 
or so (no time before then). The possible change is from:

https://stat.ethz.ch/pipermail/r-sig-geo/2015-November/023656.html

and affected writing - before Shapefiles were written as-is, from 1.1-1 
all output geometries without comments are put through 
OGRGeometryFactory::organizePolygons() in GDAL/OGR. This may be a 
case in which the OGR function fails to organise the polygons in the 
intended fashion. I have a build of rgdal 1.1-2 for Windows using GDAL 
2.0.1 (thanks again to Brian Ripley) which you may try, but it will most 
likely not change anything. Also, we don't know whether the input data 
(Polygons objects) have comments or not, but if read through readOGR(), 
the Shapefile driver also runs OGRGeometryFactory::organizePolygons() on 
read.

I need access to the offending shapefile to see whether alternative 
settings to OGRGeometryFactory::organizePolygons(), or a user option to 
avoid this very sensible function with possibly bad data, might alleviate 
the problem. Please put on URL or attach offlist.

Roger

> With your shapefile I can reproduce your problem under Windows 7x64 in R
> 3.2.2 rgdal_1.1-1 sp_1.2-1, but not R 3.1.2 rgdal_0.9-3 sp_1.1-1 or
> earlier.  Both rgdals are linked to gdal 1.11.2 released 2015/02/10.
> I also can reproduce the issue writing to & reading from GeoJSON instead of
> shapefiles.  Files written by rgdal 1.1-1 have the lines connecting holes
> when read by rgdal_0.9-3, but files written by rgdal_0.9-3 are read fine by
> 1.1-1.
>
> The rarity about the shapefile in question is that it has 57 holes in the
> same polygon, which (along with the lines connecting holes) suggests that
> the issue might be related to SpatialPolygons not assigning holes to
> specific (non-hole) polygons, see:
> http://finzi.psych.upenn.edu/R/library/rgeos/html/comment-functions.html
>
> I don't have time (or ability) to go much further right now in terms of
> finding the change, but perhaps someone else can?
>
> Tom 2
>
> On Fri, Dec 4, 2015 at 2:34 PM, Michael Sumner <mdsumner at gmail.com> wrote:
>
>>
>>
>> On Sat, 5 Dec 2015 at 05:26 Worrall, James -FS <jworrall at fs.fed.us> wrote:
>>
>>> [image: image001.gif]
>>>
>>> We have been happily using rgdal to read and write ESRI Shapefiles.
>>> Recently my colleague began using it.  We noticed that after saving and
>>> reopening files, many polygons had been reconfigured, as if the order of
>>> the vertices had become jumbled and there were many straight lines cutting
>>> across the polygon.  I’m not sure if an image can be pasted in this list
>>> but I’ll try.
>>>
>>> I did the same thing on my computer and the problem did not occur.  We
>>> found that I had an older version of rgdal, 1.0-7.  When I updated it to
>>> 1.1-1, the problem occurred just as it had with her.
>>>
>>> Simply opening and saving a shapefile causes the problem and essentially
>>> jumbles the shapefile.  The bug, if it is one, was introduced after 1.0-7
>>>
>>
>>
>>
>>
>> I can't reproduce this. Can you provide a reproducible example?  Also,
>> "opening and saving a shapefiles" is not the way to describe what is done
>> in the usual rgdal workflow, so it's not clear what you did. Here's what I
>> tried:
>>
>> library(maptools)
>> data(wrld_simpl)
>>
>> library(rgdal)
>> #rgdal: version: 1.1-1, (SVN revision 572)
>> # Geospatial Data Abstraction Library extensions to R successfully loaded
>> # Loaded GDAL runtime: GDAL 1.11.2, released 2015/02/10
>> # Path to GDAL shared files: E:/inst/R/R/library/rgdal/gdal
>> # GDAL does not use iconv for recoding strings.
>> # Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]
>> # Path to PROJ.4 shared files: E:/inst/R/R/library/rgdal/proj
>> # Linking to sp version: 1.2-1
>>
>>
>> writeOGR(wrld_simpl, ".", "1.1-1", "ESRI Shapefile")
>> x1 <- readOGR(".", "1.1-1")
>> plot(x1)  ## all good
>>
>>
>>  sessionInfo()
>> R version 3.2.2 Patched (2015-08-27 r69201)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 8.1 x64 (build 9600)
>>
>> locale:
>> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
>> [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_Australia.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] rgdal_1.1-1     maptools_0.8-37 sp_1.2-1
>>
>> loaded via a namespace (and not attached):
>> [1] tools_3.2.2     foreign_0.8-66  grid_3.2.2      lattice_0.20-33
>>
>>
>> Cheers, Mike.
>>
>>
>>
>>
>>> I will attach images of one complex polygon, before and after saving with
>>> writeOGR.
>>>
>>> Jim
>>>
>>>
>>> _______________________________________________
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>>> R-sig-Geo at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
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-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no