[R-sig-Geo] rgrass7 : Error in parseGRASS
Roger Bivand
Roger.Bivand at nhh.no
Thu Nov 24 10:48:47 CET 2016
On Thu, 24 Nov 2016, Michael DELORME wrote:
> That's great Chris, it works fine as is !
> Thank you, I don't have to keep another GRASS install aside then.
Thanks for confirming this. I'll try to set up a test rig to allow
initGRASS to set up the environment variables when using GRASS in OSGeo4W
for a later release.
Roger
>
> 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]]
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> R-sig-Geo mailing list
>>>>>>>>> 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
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>>>>>>>
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>>>>>>>
>>>>>>> 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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--
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
http://orcid.org/0000-0003-2392-6140
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