spgrass6 and GIS_LOCK

Question

I would like to thank's everyone first, i learn a lot here (gis.stackexchange) about GIS. I have one question about the use of GRASS within R session, i'm able to do some basic task, but i have one important issue is to use GRASS graphics through spgrass6::execGRASS.

I'm aware of the capabilities of R in graphics (lattice, ggplot and others), but i would like to be able to use GRASS graphics because of some option like nviz.

Here is a minimal exemple

require(spgrass6)
require(spatstat)
# to use SpatialGridDataFrame in ggplot
fortify.SpatialGridDataFrame <- function(data) as.data.frame(as.im(as.image.SpatialGridDataFrame(data)))

# initialisation and the use of spearfish60 data
initGRASS(gisBase = "/usr/lib/grass64", home = tempdir(), gisDbase = "/home/dickoa/GIS/grass/grassdata/", location = "spearfish60", mapset = "usr1", override = TRUE)

# verif
gmeta6()

execGRASS("g.list", parameters = list(type = "vect"))

parseGRASS("d.mon")

# and this command gave me errors
execGRASS("d.mon", parameters = list(start="x0"))

and the error message is :

ERREUR :Unable to get GIS_LOCK enviroment variable value

And generaly, i really like the R workflow using emacs (ESS) and the idea of keeping everything in script, it's one of the main raison for me to use grass within R, so i want also to ask for other R and GRASS users if this integration through spgrass6 (Bivand 2011) can allow me to do everything as in interactive session of GRASS.

here is my R session info (i use Kubuntu 10.10 as OS)

R version 2.12.2 (2011-02-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] spgrass6_0.6-26 XML_3.2-0       rgdal_0.6-33   
 [4] sp_0.9-79       spatstat_1.21-5 deldir_0.0-13  
 [7] mgcv_1.7-4      ggplot2_0.8.9   proto_0.3-9    
[10] reshape_0.8.4   plyr_1.4        MASS_7.3-11    

loaded via a namespace (and not attached):
[1] lattice_0.19-17    Matrix_0.999375-48 nlme_3.1-98 

Answer 1

It is way easier to call R within a GRASS session. Then you don't have to set much since R will figure out by itself. See here for examples: http://grass.osgeo.org/wiki/R_statistics

If you want instead to call R-GRASS functionality as R batch job, this should work:

library(spgrass6)

# initialisation and the use of spearfish60 data
initGRASS(gisBase = "/usr/local/grass-6.4.1", home = tempdir(), 
          gisDbase = "/home/neteler/grassdata/",
          location = "spearfish60", mapset = "user1", SG="elevation.dem",
          override = TRUE)

system("g.region -d")
# verify
gmeta6()

spear <- readRAST6(c("geology", "elevation.dem"),
          cat=c(TRUE, FALSE), ignore.stderr=TRUE,
          plugin=NULL)

summary(spear$geology)

Run this script with

R CMD BATCH batch.R

The result is (shorted here):

cat batch.Rout

R version 2.10.0 (2009-10-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
...
> library(spgrass6)
Loading required package: sp
Loading required package: rgdal
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.7.2, released 2010/04/23
Path to GDAL shared files: /usr/local/share/gdal
Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009
Path to PROJ.4 shared files: (autodetected)
Loading required package: XML
GRASS GIS interface loaded with GRASS version: (GRASS not running)
> 
> # initialisation and the use of spearfish60 data
> initGRASS(gisBase = "/usr/local/grass-6.4.1", home = tempdir(), gisDbase = "/home/neteler/grassdata/",
+           location = "spearfish60", mapset = "user1", SG="elevation.dem", override = TRUE)
gisdbase    /home/neteler/grassdata/ 
location    spearfish60 
mapset      user1 
rows        477 
columns     634 
north       4928010 
south       4913700 
west        589980 
east        609000 
nsres       30 
ewres       30 
projection  +proj=utm +zone=13 +a=6378206.4 +rf=294.9786982 +no_defs
+nadgrids=/usr/local/grass-6.4.1/etc/nad/conus +to_meter=1.0 
Warning messages:
1: In dir.create(gisDbase) : '/home/neteler/grassdata' already exists
2: In dir.create(loc_path) :
  '/home/neteler/grassdata//spearfish60' already exists
> 
> system("g.region -d")
> # verify
> gmeta6()
gisdbase    /home/neteler/grassdata/ 
location    spearfish60 
mapset      user1 
rows        477 
columns     634 
north       4928010 
...
> 
> spear <- readRAST6(c("geology", "elevation.dem"),
+           cat=c(TRUE, FALSE), ignore.stderr=TRUE,
+           plugin=NULL)
> 
> summary(spear$geology)
metamorphic  transition     igneous   sandstone   limestone       shale 
      11693         142       36534       74959       61355       46423 
sandy shale    claysand        sand        NA's 
      11266       14535       36561        8950 
> 
> 
> proc.time()
   user  system elapsed 
  2.891   0.492   3.412 

Hope this helps.