[R-sig-Geo] rgrass7 : Error in parseGRASS

Tue Nov 22 15:13:54 CET 2016

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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>>> 165 rue Garibaldi – BP 3202 – 69401 LYON cedex 03
>>> 04 78 63 34 21
>>>
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>>>
>>> http://www.draaf.auvergne-rhone-alpes.agriculture.gouv.fr/
>>>
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>>>
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>>
>
>
>

-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
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