[R-sig-Geo] rgrass7 : Error in parseGRASS
Michael DELORME
michael.delorme at agriculture.gouv.fr
Thu Nov 24 10:40:13 CET 2016
That's great Chris, it works fine as is !
Thank you, I don't have to keep another GRASS install aside then.
I'm sure it will be helpful to other people also.
Thanks again
Le 24/11/2016 09:17, Chris Reudenbach a écrit :
> 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 écrit :
>>> 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 écrit :
>>>>> 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 écrit :
>>>>>>> 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'accés
>>>>>>>> spécifié 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'accés
>>>>>>>> spécifié 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> [[alternative HTML version deleted]]
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>> R-sig-Geo at r-project.org
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>> --
>>>>>> *Michaël DELORME*
>>>>>> Administrateur de données, chargé de projet en géomatique
>>>>>> Service régional de l'information statistique, économique et
>>>>>> territoriale
>>>>>> Direction régionale de l'alimentation, de l'agriculture et de la
>>>>>> forêt
>>>>>> Auvergne-Rhône-Alpes
>>>>>> Site de Lyon
>>>>>> 165 rue Garibaldi – BP 3202 – 69401 LYON cedex 03
>>>>>> 04 78 63 34 21
>>>>>>
>>>>>> Pour écrire au service :
>>>>>> DRAAF Auvergne-Rhône-Alpes – SRISET
>>>>>> 16B rue Aimé Rudel – BP 45 – 63370 LEMPDES
>>>>>>
>>>>>> http://www.draaf.auvergne-rhone-alpes.agriculture.gouv.fr/
>>>>>>
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>>>>>>
>>>>>> _______________________________________________
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>>>>
>>>>
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--
*Michaël DELORME*
Administrateur de données, chargé de projet en géomatique
Service régional de l'information statistique, économique et territoriale
Direction régionale de l'alimentation, de l'agriculture et de la forêt
Auvergne-Rhône-Alpes
Site de Lyon
165 rue Garibaldi – BP 3202 – 69401 LYON cedex 03
04 78 63 34 21
Pour écrire au service :
DRAAF Auvergne-Rhône-Alpes – SRISET
16B rue Aimé Rudel – BP 45 – 63370 LEMPDES
http://www.draaf.auvergne-rhone-alpes.agriculture.gouv.fr/
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