[GRASS-stats] rgrass7 read/write SpatialPolygonsDataFrames errors

Fri Oct 9 07:04:10 PDT 2015

Roger, with GRASS version 7.0.1 and rgrass7_0.1-3, readVECT now doesn't ask
for the driver to use but gives the same error as before:

writeVECT(SDF = mz.pol, vname = zm.pol, v.in.ogr_flags = "o")
Over-riding projection check
Check if OGR layer <q7468fb> contains polygons...

Importing 205 features (OGR layer <q7468fb>)...

-----------------------------------------------------
Registering primitives...
3924 primitives registered
12866 vertices registered
Number of nodes: 2884
Number of primitives: 3924
Number of points: 0
Number of lines: 0
Number of boundaries: 3924
Number of centroids: 0
Number of areas: -
Number of isles: -
-----------------------------------------------------
Cleaning polygons
-----------------------------------------------------
Breaking polygons...
Breaking polygons (pass 1: select break points)...

Breaking polygons (pass 2: break at selected points)...

-----------------------------------------------------
Removing duplicates...

-----------------------------------------------------
Breaking boundaries...

-----------------------------------------------------
Removing duplicates...

-----------------------------------------------------
Cleaning boundaries at nodes...

-----------------------------------------------------
Merging boundaries...

-----------------------------------------------------
Removing dangles...

-----------------------------------------------------
Building areas...

205 areas built
13 isles built
Number of nodes: 2929
Number of primitives: 7268
Number of points: 0
Number of lines: 0
Number of boundaries: 7268
Number of centroids: 0
Number of areas: 205
Number of isles: 13
-----------------------------------------------------
Removing bridges...

-----------------------------------------------------
Registering primitives...
498 primitives registered
5828 vertices registered
Building areas...

205 areas built
13 isles built
Attaching islands...

Number of nodes: 306
Number of primitives: 498
Number of points: 0
Number of lines: 0
Number of boundaries: 498
Number of centroids: 0
Number of areas: 205
Number of isles: 13
-----------------------------------------------------
Finding centroids for OGR layer <q7468fb>...

-----------------------------------------------------
Writing centroids...

-----------------------------------------------------
205 input polygons
Total area: 1.25187E+006 (205 areas)
-----------------------------------------------------
Copying features...

WARNING: Unable to delete file

 'C:/Users/ediez1/AppData/Local/Temp/Rtmpqkeay4/file480c1e5e16a7/file480c11cc233b/.tmp/unknown/vector/tmp_8308/coor'
Building topology for vector map <q7468fb at file480c11cc233b>...
Registering primitives...
703 primitives registered
6033 vertices registered
Building areas...

205 areas built
13 isles built
Attaching islands...

Attaching centroids...

Number of nodes: 306
Number of primitives: 703
Number of points: 0
Number of lines: 0
Number of boundaries: 498
Number of centroids: 205
Number of areas: 205
Number of isles: 13
> execGRASS("v.clean", flags = c("overwrite"), input = zm.pol,
+ output = zm.gnrl, tool = "rmarea", threshold = 3000)
--------------------------------------------------
Tool: Threshold
Remove small areas: 3000
--------------------------------------------------
Copying features...

Rebuilding parts of topology...
Building topology for vector map <u10f44b at file480c11cc233b>...
Registering primitives...
703 primitives registered
6033 vertices registered
Building areas...

205 areas built
13 isles built
Attaching islands...

Attaching centroids...

Number of nodes: 306
Number of primitives: 703
Number of points: 0
Number of lines: 0
Number of boundaries: 498
Number of centroids: 205
Number of areas: 205
Number of isles: 13
--------------------------------------------------
Tool: Remove small areas

174 areas of total size 50601.7 removed
--------------------------------------------------
Rebuilding topology for output vector map...
Building topology for vector map <u10f44b at file480c11cc233b>...
Registering primitives...
333 primitives registered
4705 vertices registered
Building areas...

31 areas built
3 isles built
Attaching islands...

Attaching centroids...

Number of nodes: 274
Number of primitives: 333
Number of points: 0
Number of lines: 0
Number of boundaries: 302
Number of centroids: 31
Number of areas: 31
Number of isles: 3
> zm.fnl <- readVECT(zm.gnrl)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
 :
  line 4 did not have 2 elements
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United
States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] RPyGeo_0.9-3    RSAGA_0.94-3    plyr_1.8.3      gstat_1.0-26
 shapefiles_0.7  foreign_0.8-65  maptools_0.8-37 rgdal_1.0-7
classInt_0.1-23
[10] raster_2.4-20   rgrass7_0.1-3   XML_3.98-1.3    sp_1.2-0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1      intervals_0.15.1 lattice_0.20-33  FNN_1.1
 spacetime_1.1-4  class_7.3-13     zoo_1.7-12       grid_3.2.2
 [9] e1071_1.6-7      xts_0.9-7        tools_3.2.2

Thanks

2015-10-08 18:57 GMT-03:00 Roger Bivand <Roger.Bivand at nhh.no>:

> Sorry this has taken a long time; please try installing the development
> version available from:
>
> http://win-builder.r-project.org/8Y3Ihj451Clx
>
> (rgrass7_0.1-3.zip). The problem was the use of "_" instead of " " in the
> name of the OGR shapefile driver - in OGR and R it is "ESRI Shapefile", in
> GRASS it is "ESRI_Shapefile". Because the new long-name work-around worked
> on systems not needing to use this driver, it wasn't properly tested - and
> on Windows the GRASS standalone has OGR with the SQLite driver, but the
> Windows rgdal binary does not have SQLite. You may wish to install the R
> RSQLite package to move data if you use long field/column names.
>
> Before installing this development version, and after library(rgrass7),
> run example(readVECT) in the basic nc location from:
>
> https://grass.osgeo.org/sampledata/north_carolina/nc_basic_spm_grass7.zip
>
> it should fail. Then restart R, install the development version of rgrass7
> from the first link, and repeat - it works for me and should resolve the
> problem.
>
> Hope this helps,
>
> Roger
>
>
> --
> Roger Bivand
> Norwegian School of Economics
> Helleveien 30, 5045 Bergen, Norway
> Roger.Bivand at nhh.no
>
>
>
>
>
> Fra: grass-stats-bounces at lists.osgeo.org [
> grass-stats-bounces at lists.osgeo.org] på vegne av Eduardo Diez [
> eduardodiez at gmx.com]
> Sendt: 24. september 2015 9:11
> Til: grass-stats at lists.osgeo.org
> Emne: [GRASS-stats] rgrass7 read/write SpatialPolygonsDataFrames errors
>
>
> Hi, I'm a user of R mostly for spatial information processing. Besides sp,
> maptools, etc. i also use functions from GRASS, at first through spgrass6
> and then rgrass7. A few days ago, I started having trouble reading and
> writing SpatialPolygonsDataFrames using readVECT and writeVECT. I tried
> both reinstalling both grass (6.4.4, 7.0.0 and 7.0.1) and the R packages
> (spgrass6 0.8-6 and rgrass7 0.1-2), and also with different R objects but i
> kept getting the same errors.
>
>
> The "mult.r" object is a RasterLayer with 4 zones and the objective is to
> convert it to polygons and "clean" small areas with v.clean rmarea (as i
> don't currently know a way of doing this in plain R).
>
>
>
> The first thing that came out strange was that when executing writeVECT it
> would ask me for the driver to use (in the way of rgdal's writeOGR, it
> didn't ask for it before). I figured out that object to be written should
> be projected (not in lat-lon, don't know why). After doing this i could
> write the vector and execute v.clean. The problem came again when trying to
> read the cleaned polygons back to R.
> Below i paste an extract of my R console with the errors and some
> information.
>
>
>
> Thanks in advance,
>
> Eduardo
>
>
> > mult.rp <- projectRaster(mult.r, crs = prj.crs, method = "ngb")
> > mult.pol <- rasterToPolygons(mult.rp, dissolve = T)
>
> > initGRASS(gisBase = "c:/Program Files (x86)/GRASS GIS 7.0.1", home =
> tempdir(), override = T)
> gisdbase    C:/Users/ediez1/AppData/Local/Temp/RtmpegbyiQ
> location    file2f7c6dc070e6
> mapset      file2f7c30eb3f52
> rows        1
> columns     1
> north       1
> south       0
> west        0
> east        1
> nsres       1
> ewres       1
> projection  NA
> > writeVECT(mult.pol, "pol1", v.in.ogr_flags = "o")
> Error: !is.null(driver) is not TRUE
> > writeVECT(mult.pol, "pol1", v.in.ogr_flags = "o", driver = "ESRI
> Shapefile")
>
> Over-riding projection check
> Check if OGR layer <r848659> contains polygons...
>
>
> Importing 4 features (OGR layer <r848659>)...
>
>
> -----------------------------------------------------
> Registering primitives...
> 3005 primitives registered
> 15587 vertices registered
> Number of nodes: 2691
> Number of primitives: 3005
> Number of points: 0
> Number of lines: 0
> Number of boundaries: 3005
> Number of centroids: 0
> Number of areas: -
> Number of isles: -
> -----------------------------------------------------
> Cleaning polygons
> -----------------------------------------------------
> Breaking polygons...
> Breaking polygons (pass 1: select break points)...
>
>
> Breaking polygons (pass 2: break at selected points)...
>
>
> -----------------------------------------------------
> Removing duplicates...
>
>
> -----------------------------------------------------
> Breaking boundaries...
>
>
> -----------------------------------------------------
> Removing duplicates...
>
>
> -----------------------------------------------------
> Cleaning boundaries at nodes...
>
>
> -----------------------------------------------------
> Merging boundaries...
>
>
> -----------------------------------------------------
> Removing dangles...
>
>
> -----------------------------------------------------
> Building areas...
>
>
> 95 areas built
> 8 isles built
> Number of nodes: 2771
> Number of primitives: 7307
> Number of points: 0
> Number of lines: 0
> Number of boundaries: 7307
> Number of centroids: 0
> Number of areas: 95
> Number of isles: 8
> -----------------------------------------------------
> Removing bridges...
>
>
> -----------------------------------------------------
> Registering primitives...
> 231 primitives registered
> 7594 vertices registered
> Building areas...
>
>
> 95 areas built
> 8 isles built
> Attaching islands...
>
>
> Number of nodes: 144
> Number of primitives: 231
> Number of points: 0
> Number of lines: 0
> Number of boundaries: 231
> Number of centroids: 0
> Number of areas: 95
> Number of isles: 8
> -----------------------------------------------------
> Finding centroids for OGR layer <r848659>...
>
>
> -----------------------------------------------------
> Writing centroids...
>
>
> -----------------------------------------------------
> 95 input polygons
> Total area: 1.28981E+006 (95 areas)
> -----------------------------------------------------
> Copying features...
>
>
> WARNING: Unable to delete file
>
>  'C:/Users/ediez1/AppData/Local/Temp/Rtmpg10lvi/filec2473b0126/filec24129b63ac/.tmp/unknown/vector/tmp_10484/coor'
> Building topology for vector map <r848659 at filec24129b63ac>...
> Registering primitives...
> 326 primitives registered
> 7689 vertices registered
> Building areas...
>
>
> 95 areas built
> 8 isles built
> Attaching islands...
>
>
> Attaching centroids...
>
>
> Number of nodes: 144
> Number of primitives: 326
> Number of points: 0
> Number of lines: 0
> Number of boundaries: 231
> Number of centroids: 95
> Number of areas: 95
> Number of isles: 8
>
>
> > execGRASS("v.clean", flags = c("overwrite"), input = "pol1",
> + output = "clnpol", tool = "rmarea", threshold = 3000)
> --------------------------------------------------
> Tool: Threshold
> Remove small areas: 3000
> --------------------------------------------------
> Copying features...
>
>
> Rebuilding parts of topology...
> Building topology for vector map <k1f9f75 at filec24129b63ac>...
> Registering primitives...
> 326 primitives registered
> 7689 vertices registered
> Building areas...
>
>
> 95 areas built
> 8 isles built
> Attaching islands...
>
>
> Attaching centroids...
>
>
> Number of nodes: 144
> Number of primitives: 326
> Number of points: 0
> Number of lines: 0
> Number of boundaries: 231
> Number of centroids: 95
> Number of areas: 95
> Number of isles: 8
> --------------------------------------------------
> Tool: Remove small areas
>
>
> 55 areas of total size 29487.1 removed
> --------------------------------------------------
> Rebuilding topology for output vector map...
> Building topology for vector map <k1f9f75 at filec24129b63ac>...
> Registering primitives...
> 212 primitives registered
> 6840 vertices registered
> Building areas...
>
>
> 40 areas built
> 4 isles built
> Attaching islands...
>
>
> Attaching centroids...
>
>
> Number of nodes: 136
> Number of primitives: 212
> Number of points: 0
> Number of lines: 0
> Number of boundaries: 172
> Number of centroids: 40
> Number of areas: 40
> Number of isles: 4
> > cln.pol <- readVECT("clnpol")
> Error: !is.null(driver) is not TRUE
> > cln.pol <- readVECT("clnpol", driver = "ESRI Shapefile")
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
> na.strings,  :
>   line 4 did not have 2 elements
>
>
> > sessionInfo()
> R version 3.2.2 (2015-08-14)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
>
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United
> States.1252
>
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> other attached packages:
> [1] rgrass7_0.1-2   classInt_0.1-22 maptools_0.8-36 ggplot2_1.0.1
>  XML_3.98-1.3    raster_2.4-20   sp_1.2-0
>
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.1      magrittr_1.5     MASS_7.3-43      munsell_0.4.2
> colorspace_1.2-6 lattice_0.20-33  stringr_1.0.0    plyr_1.8.3
>  [9] tools_3.2.2      parallel_3.2.2   rgdal_1.0-7      grid_3.2.2
>  gtable_0.1.2     e1071_1.6-7      class_7.3-13     rgeos_0.3-12
> [17] digest_0.6.8     reshape2_1.4.1   labeling_0.3     stringi_0.5-5
> scales_0.3.0     foreign_0.8-65   proto_0.3-10
>
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