rgrass7 : Error in parseGRASS

Michael,

Using a fresh OSGEO4W64 standard quick desktop installation (i.e.
installation of the default desktop GIS software packages with the
installer and using C:\OSGeo4W64 as path)  I suggest the below solution.

You have to set all necessary eniromental and system variables
manually. I am not quit sure if I got them but actually it seems to
work for your question. As a conclusion I think your Python and all of
the rest is installed correct.


cheers Chris


############### librarys, data etc
---------------------------------------------
library(rgrass7)
library(sp)

# setup a temp workingdir
working.dir<- "~/tmp/"

# get meuse data

data(meuse)
data(meuse.grid)

# georeference the meuse grid data
coordinates(meuse.grid) <- ~x+y
proj4string(meuse.grid) <- CRS("+init=epsg:28992")
gridded(meuse.grid) <- TRUE

# get a first cellsize/pixel resolution for GRASS
resolution <- meuse.grid at grid@cellsize[1]

# georeference the meuse data
coordinates(meuse) <- ~x+y
proj4string(meuse) <- CRS("+init=epsg:28992")

# get projection, proj4 string and extent for GRASS
projection<-(strsplit(meuse at proj4string@projargs,split = " "))
proj4<- paste(projection[[1]][2:length(unlist(projection))], collapse
= ' ')
xmax<-meuse at bbox[3]
xmin<-meuse at bbox[1]
ymax<-meuse at bbox[4]
ymin<-meuse at bbox[2]

# create and set working directory
if (!file.exists(file.path(working.dir,"run"))){
  dir.create(file.path(working.dir,"run"),recursive = TRUE)
}
setwd(file.path( working.dir,"run"))


########### SETUP OSGEO4W enviroment settings manually
-------------------------
# setup the OSGEO4W environ manually
# assuming a osgeow4w default "deskop fastinstall
# using the default installation directory "C:\OSGeo4W64"

# set OSGE4W base directory
osgeo4w.root<-"C:\\OSGEO4~1"
Sys.setenv(OSGEO4W_ROOT=osgeo4w.root)
# define GISBASE
grass.gis.base<-paste0(osgeo4w.root,"\\apps\\grass\\grass-7.0.5")
Sys.setenv(GISBASE=grass.gis.base)

Sys.setenv(GRASS_PYTHON=paste0(Sys.getenv("OSGEO4W_ROOT"),"\\bin\\python.exe"))

Sys.setenv(PYTHONHOME=paste0(Sys.getenv("OSGEO4W_ROOT"),"\\apps\\Python27"))

Sys.setenv(PYTHONPATH=paste0(Sys.getenv("OSGEO4W_ROOT"),"\\apps\\grass\\grass-7.0.5\\etc\\python"))

Sys.setenv(GRASS_PROJSHARE=paste0(Sys.getenv("OSGEO4W_ROOT"),"\\share\\proj"))

Sys.setenv(PROJ_LIB=paste0(Sys.getenv("OSGEO4W_ROOT"),"\\share\\proj"))
Sys.setenv(GDAL_DATA=paste0(Sys.getenv("OSGEO4W_ROOT"),"\\share\\gdal"))
Sys.setenv(GEOTIFF_CSV=paste0(Sys.getenv("OSGEO4W_ROOT"),"\\share\\epsg_csv"))

Sys.setenv(FONTCONFIG_FILE=paste0(Sys.getenv("OSGEO4W_ROOT"),"\\etc\\fonts.conf"))


# call all OSGEO4W settings
system("C:/OSGeo4W64/bin/o-help.bat")


# create PATH variable
Sys.setenv(PATH=paste0(grass.gis.base,";",
"C:\\OSGEO4~1\\apps\\Python27\\lib\\site-packages\\numpy\\core",";",
"C:\\OSGeo4W64\\apps\\grass\\grass-7.0.5\\bin",";",
"C:\\OSGeo4W64\\apps\\grass\\grass-7.0.5\\lib",";",
"C:\\OSGeo4W64\\apps\\grass\\grass-7.0.5\\etc",";",
"C:\\OSGeo4W64\\apps\\grass\\grass-7.0.5\\etc\\python",";",
"C:\\OSGeo4W64\\apps\\Python27\\Scripts",";",
                       "C:\\OSGeo4W64\\bin",";",
                       "c:\\OSGeo4W64\\apps",";",
                       "C:\\OSGEO4~1\\apps\\saga",";",
                       paste0(Sys.getenv("WINDIR"),"/WBem"),";",
                       Sys.getenv("PATH")))


#################### start with GRASS setup
------------------------------------
rgrass7::initGRASS(gisBase=grass.gis.base,
                   home=tempdir(),
                   mapset='PERMANENT',
                   override=TRUE
)

# assign GRASS projection according to data set
rgrass7::execGRASS('g.proj',
                   flags=c('c','quiet'),
                   proj4=proj4
)

# assign GRASS extent and resolution
rgrass7::execGRASS('g.region',
                   flags=c('quiet'),
                   n=as.character(ymax),
                   s=as.character(ymin),
                   e=as.character(xmax),
                   w=as.character(xmin),
                   res=as.character(resolution)
)


#############   now do GRASS STUFF
---------------------------------------------

rgrass7::writeVECT(meuse,"meuse")
rgrass7::execGRASS("v.db.addcolumn", map = "meuse", columns = "area_m2
double
                   precision")
#############  do other command line stuff
-------------------------------------

## call gdal
system("gdal_merge")

# call saga cli
system("saga_cmd")


Am 23.11.2016 um 07:38 schrieb Michael DELORME:

Thanks for your insight.
I'll use a stand-alone GRASS install.

Cordially

Le 22/11/2016 15:13, Roger Bivand a ?crit :

On Tue, 22 Nov 2016, Michael DELORME wrote:

Thanks for investigating.

I'll try a standalone version of GRASS if needed.

Here is the traceback

traceback()

4: stop(paste(cmd, "not parsed"))
3: parseGRASS(cmd, legacyExec = legacyExec)
2: doGRASS(cmd, flags = flags, ..., parameters = parameters, echoCmd =
echoCmd, legacyExec = legacyExec)
1: execGRASS("v.db.addcolumn", map = "meuse", columns = "area_m2
double
precision")

My C:\OSGeo4W64\apps\grass\grass-7.0.5\bin lists *.exe or *.bat and
indeed the *.bat command are those which don't work (r.mask.bat,
v.db.addcolumn.bat,...). The batch calls Python scripts ; for example
v.db.addcolumn.bat is :

@"%GRASS_PYTHON%" "%GISBASE%/scripts/v.db.addcolumn.py" %*

So I guess something must be wrong in my Python installation... (it
works however from within a GRASS shell)

No, the logic for Windows and initGRASS has only ever been tested with
stand-alone GRASS. I would guess that in OSGeo4W the path variables
are wrong. I cannot even find out how to run initGRASS in R but
outside the OSGeo4W shell (doesn't find iconv.dll) or inside the
OSGeo4W shell (cannot create a temporary GRASS location). Unless you
or others really need OSGeo4W, I suggest asking others to implement
that - very bulky and fragile.

Roger

Cordially


Le 22/11/2016 14:30, Roger Bivand a ?crit :

On Tue, 22 Nov 2016, Michael DELORME wrote:

Thanks for replying

Here is a reproducible example (change your GRASS directory of
course) :

library(rgrass7)
library(sp)
initGRASS("C:/OSGeo4W64/apps/grass/grass-7.0.5", home = tempdir(),
override = TRUE)
data(meuse)
coordinates(meuse) <- ~x+y
writeVECT(meuse, "meuse")
execGRASS("v.db.addcolumn", map = "meuse", columns = "area_m2 double
precision")

This appears to run correctly on Windows 7 with GRASS 7.0.5 Windows
stand-alone. Do you need to use OSGeo4W - the internal logic used for
finding out where the different versions keep their executables and
batch files varies?

What does traceback() say after the error? The error comes from
parseGRASS("v.db.addcolumn") - the XML error comes from not being
able
to read the output of v.db.addcolumn<.ext> --interface-description
where <.ext> may be .exe or .bat I think.

Roger

I get :
Error : XML content does not seem to be XML: 'The specified path
was not
found.'
In addition: Warning message:
running command 'v.db.addcolumn.bat --interface-description' had
status 1
Error in parseGRASS(cmd, legacyExec = legacyExec) :
  v.db.addcolumn not parsed

Other execGRASS commands (like r.neighbors, r.mapcalc,..)  work
fine,
but some other (r.mask) fail with a similar XML error.

All commands work fine when used from the GRASS shell...

What is this XML error ?
Thanks

Le 22/11/2016 09:34, Roger Bivand a ?crit :

On Tue, 22 Nov 2016, Michael DELORME wrote:

Dear list,

Using rgrass7 on Windows7 with GRASS 7.0.5 (OSGeo distribution),
I get
the following error :

Please always try to provide a reproducible example using a
standard
data set. In addition, the output of traceback() following the
error
would be helpful. Are you running R inside GRASS, or using R to
initiate GRASS?

Consider using the grass-stats list:

https://lists.osgeo.org/mailman/listinfo/grass-stats

as it is more likely to yield results, but there also provide an
example that anyone can reproduce. The example should avoid loading
other packages, and should be run from the R console (not, say,
RStudio).

Roger

execGRASS("v.db.addcolumn", map = "result_v", columns = "area_m2
double precision")

Error : XML content does not seem to be XML: 'Le chemin d'acc?s
sp?cifi? est introuvable.' In addition: Warning message: running
command 'v.db.addcolumn.bat --interface-description' had status 1
Error in parseGRASS(cmd, legacyExec = legacyExec) :
  v.db.addcolumn not parsed


and a similar one for r.mask :

execGRASS("r.mask", raster = "map")

Error : XML content does not seem to be XML: 'Le chemin d'acc?s
sp?cifi? est introuvable.'
In addition: Warning message:
running command 'r.mask.bat --interface-description' had status 1
Error in parseGRASS(cmd, legacyExec = legacyExec) : r.mask not
parsed


whereas most other execGRASS command I tried work as expected.
Any idea ?
Thanks in advance

Here is my session info :

sessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
LC_MONETARY=French_France.1252 LC_NUMERIC=C [5]
LC_TIME=French_France.1252
attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets
methods   base
other attached packages: [1] rgrass7_0.1-9 XML_3.98-1.4 beepr_1.2
raster_2.5-8 sp_1.2-3 RPostgreSQL_0.4-1 DBI_0.5-1

loaded via a namespace (and not attached): [1] magrittr_1.5
tools_3.3.1 audio_0.1-5 Rcpp_0.12.7 stringi_1.1.2 grid_3.3.1
stringr_1.1.0 lattice_0.20-34 [9] fortunes_1.5-3



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*Micha?l DELORME*
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