[GRASS-stats] GRASS-R connection in Windows

[Helmut Kudrnovsky]

Hi Antonio,

I've been using WinGRASS for a while but now I would like to run a few 
functions from R using spgrass (interface between GRASS and R).
I know that this is possible and stable in Linux but I'm not sure for 
Windows. Has anyone tried?
Thanks
Antonio

at the moment there is following for a Grass-R-connection in implemented in 
WinGrass64

(1) the WinGrass64-installer searches during installation for a installed R and 
writes - if found - the
R-installation-path to %PATH% in the grass64.bat-starting script
(see 
http://trac.osgeo.org/grass/browser/grass/branches/develbranch_6/mswindows/GRASS-Installer.nsi#L660)

(2) you can start Grass-command-line - it's a windows-command-line, not a 
msys-rxvt-terminal (you can find this
starting option under Programs - Grass64 - Grass command line; but not as a 
desktop icon)

with this starting option you start a Grass-session in the good old text mode. 
if you type R in the
command line, then you start R inside a Grass-session like in Linux. see down:

Welcome to GRASS 6.4.0 (2010)

GRASS homepage:  http://grass.osgeo.org/
This version running thru:   Windows Command Shell (cmd.exe)
When ready to quit enter:exit
Help is available with the command:  g.manual -i
See the licence terms with:  g.version -c

Microsoft Windows [Version 6.0.6002]
Copyright (c) 2006 Microsoft Corporation. Alle Rechte vorbehalten.

GRASS 6.4.0 (wgs84gc) R

R version 2.11.1 (2010-05-31)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten.
Tippen Sie 'license()' or 'licence()' für Details dazu.

R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
Tippen Sie 'contributors()' für mehr Information und 'citation()',
um zu erfahren, wie R oder R packages in Publikationen zitiert werden können.

Tippen Sie 'demo()' für einige Demos, 'help()' für on-line Hilfe, oder
'help.start()' für eine HTML Browserschnittstelle zur Hilfe.
Tippen Sie 'q()', um R zu verlassen.

 q()
Workspace sichern? [y/n/c]: n

GRASS 6.4.0 (wgs84gc)

what I have in mind (but no time at the moment to improve), see:

Ticket #1103 (new enhancement) WinGrass64 - windows-commandline not released
Ticket #1149 (new enhancement) WinGrass - load R-installation-path dynamically 
into PATH

with #1103 a Grass-session with wxGui, command-line and R inside a 
Grass-session would
be possible (as already does in WinGrass7)

with #1149 Wingrass would recognize also an upgraded R-installation (which does 
not at the moment)

best regards
Helmut
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[GRASS-stats] Re: GRASS-R connection in Windows

[Helmut Kudrnovsky]

Hi Antonio

-Ursprüngliche Nachricht-
Von: António Rocha 
Gesendet: 27.09.2010 11:27:43
An: Helmut Kudrnovsky
Betreff: Re: GRASS-R connection in Windows

Hello Helmut
First of all, let me thank you for your reply.

de nada

Helmut Kudrnovsky wrote:

 (2) you can start Grass-command-line - it's a windows-command-line, not a 
 msys-rxvt-terminal (you can find this
 starting option under Programs - Grass64 - Grass command line; but not as 
 a desktop icon)
   
Here I have a question: Is it possible to run a GRASS-Python Script with 
R-commands just like a normal GRASS-Python Script? (without having to 
run R in command-line)- I believe it has to do with Ticket #1103 right?

Best regards,
Antonio Rocha

sorry, but I've never used Grass, R and python together. so it's outside of my 
knowledge. maybe drop this question
also at the user- and/or dev-mailing-list.

at the moment for WinGrass, the R-installation-path is recognized only once at 
the WinGrass-installation-procedure and set into the %PATH-variable, 
so no future upgrade of a R-version will be recognized by the 
wingrass-installation.

the intention of ticket #1103 would be to set the R-installation-path 
dynamically at every start of a grass-session.

best regards
Helmut
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Re: [GRASS-stats] Re: GRASS-R connection in Windows

[Helmut Kudrnovsky]

Hi,

I've tried to install spgrass6 in my Windows-R.2.11.1, there seems to be no 
problem. see down. please contact the r-user-ml for R-related problems.

best regards
Helmut

___
R version 2.11.1 (2010-05-31)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten.
Tippen Sie 'license()' or 'licence()' für Details dazu.

R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
Tippen Sie 'contributors()' für mehr Information und 'citation()',
um zu erfahren, wie R oder R packages in Publikationen zitiert werden können.

Tippen Sie 'demo()' für einige Demos, 'help()' für on-line Hilfe, oder
'help.start()' für eine HTML Browserschnittstelle zur Hilfe.
Tippen Sie 'q()', um R zu verlassen.

 chooseCRANmirror()
 install.packages(spgrass6, dependencies=TRUE)
Warnung in install.packages(spgrass6, dependencies = TRUE) :
 Argument 'lib' fehlt: nutze 'C:\Users\syringia\Documents/R/win-library/2.11'
versuche URL 
'http://cran.at.r-project.org/bin/windows/contrib/2.11/spgrass6_0.6-20.zip'
Content type 'application/zip' length 367628 bytes (359 Kb)
URL geöffnet
downloaded 359 Kb

Paket 'spgrass6' erfolgreich ausgepackt und MD5 Summen abgeglichen

Die heruntergeladenen Pakete sind in 
 C:\Users\syringia\AppData\Local\Temp\RtmpzLFz82\downloaded_packages
 

_



-
Von: Abdoul Dia 
Gesendet: 27.09.2010 19:00:00
An: António Rocha
Betreff: Re: [GRASS-stats] Re: GRASS-R connection in Windows


Hi everyone,
 
I'm wondering if I can ask my question here as I'm not sure to be on the right 
place?! I'm trying to connect Grass 6.4 with R.2.11 so I can use spgrass6 and 
GRASS packages under R but I can't get the gmeta() or gmeta6() output. I can't 
even install spgrass6 on linux. I tried on windows as well as on linux (ubuntu 
karmic). Is there someone who faced such a problem and how can I solve?
 
Thanks in advance.
 
Abdoul O. Dia


2010/9/27 António Rocha [antonio.ro...@deimos.com.pt]

Hello Helmut
First of all, let me thank you for your reply.




Helmut Kudrnovsky wrote:


(2) you can start Grass-command-line - it's a windows-command-line, not a 
msys-rxvt-terminal (you can find this
 starting option under Programs - Grass64 - Grass command line; but not as a 
desktop icon)
 


Here I have a question: Is it possible to run a GRASS-Python Script with 
R-commands just like a normal GRASS-Python Script? (without having to run R in 
command-line)- I believe it has to do with Ticket #1103 right?

Best regards,
Antonio Rocha


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[GRASS-stats] [GRASS-user] WinGRASS 7-R-integration

[Helmut Kudrnovsky]

hi,

in WinGRASS 7 (standalone installer:
http://grass.osgeo.org/download/software.php#g70x) the Windows batchfiles
for use with R (http://code.google.com/p/batchfiles/) are now integrated for
a smooth GRASS-R-coupling in windows.

see also trac.osgeo.org/grass/ticket/1149

and for the usage see

http://grass.osgeo.org/wiki/R_statistics#Usage_III



-
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Helmut
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Re: [GRASS-stats] Using GRASS addons in R on Windows

[Helmut Kudrnovsky]

>Wrong target, please use:
>http://win-builder.r-project.org/s90s00N7rhyt/rgrass7_0.1-4.zip

> utils:::menuInstallLocal()
Paket ‘rgrass7’ erfolgreich ausgepackt und MD5 Summen abgeglichen

GRASS version: 7.1.svn  
GRASS SVN revision: 67543   
Build date: 2016-01-11  
Build platform: x86_64-w64-mingw32  
GDAL: 1.11.3
PROJ.4: 4.9.2   
GEOS: 3.5.0 
SQLite: 3.7.17  
Python: 2.7.5   
wxPython: 2.8.12.1  
Platform: Windows-7-6.1.7601-SP1

> library(rgrass7)
Loading required package: sp
Loading required package: XML
GRASS GIS interface loaded with GRASS version: GRASS 7.1.svn (2016)
and location: nc_spm_08_grass7

--
binary addon (r.stream.order)

> execGRASS("r.watershed", elevation="elevation", threshold=1,
> accumulatio$
SECTION 1a (of 5): Initiating Memory.
SECTION 1b (of 5): Determining Offmap Flow.
 100%
SECTION 2: A* Search.
 100%
SECTION 3a: Accumulating Surface Flow with MFD.
 100%
SECTION 3b: Adjusting drainage directions.
 100%
SECTION 4: Watershed determination.
 100%
SECTION 5: Closing Maps.
 100%
>

> execGRASS("r.stream.order", stream_rast="mystreams",
> direction="myflowdir", $
All in RAM calculation...
Reading raster map ...
 100%
Reading raster map ...
 100%
Finding nodes...
Calculating Strahler's stream order...
Writing output raster maps...
--
python addon (r.roughness.vector):

> execGRASS("r.slope.aspect", elevation="elevation", slope="myslope",
> aspect="$
 100%
Aspect raster map  complete
Slope raster map  complete

> execGRASS("r.roughness.vector", elevation="elevation", slope="myslope",
> aspe$
Error in system(cmd0, intern = TRUE) : 'r.roughness.vector.exe' not found
Error in parseGRASS(cmd, legacyExec = legacyExec) :
  r.roughness.vector not found
--
python GRASS script (r.reclass.area):

> execGRASS("r.reclass.area", input="zipcodes",
> output="zipcode_larger2000ha",$
Error in system(cmd0, intern = TRUE) : 'r.reclass.area.exe' not found
Error in parseGRASS(cmd, legacyExec = legacyExec) :
  r.reclass.area not found
--

it seems to be the same behaviour: 

binary addons (exe living in e.g.
C:\Users\xy\AppData\Roaming\GRASS7\addons\bin) are found.
python scripts (with related bat-files in e.g.
C:\Users\xy\AppData\Roaming\GRASS7\addons\bin or in e.g. C:\Program
Files\GRASS GIS 7.1.svn\bin) are not found as it is searched for e.g.
r.reclass.area.exe (see above).



-
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Re: [GRASS-stats] Using GRASS addons in R on Windows

[Helmut Kudrnovsky]

>OK. Please check that r.roughness.vector.bat is present in:
>
>C:\Users\xy\AppData\Roaming\GRASS7\addons\bin, or
>C:\Program Files\GRASS GIS 7.1.svn\bin 

it is in the addon path: C:\Users\xxx\AppData\Roaming\GRASS7\addons\bin

it works in winGRASS itself.

r.roughness.vector elevation=elevation@PERMANENT slope=slope@rtestw64bit
aspect=aspect@rtestw64bit

Check if input files exist ...

Define default output names when not defined by user ...

Calculate compass aspect values ...

Calculate colatitude ...

Calculate direction cosines ...

Calculate sum of direction cosines ...
Calculating sum of X direction cosines ...
Calculating sum of Y direction cosines ...
Calculating sum of Z direction cosines ...

Calculate vector strength ...

Calculate inverted Fisher's K parameter ...

Result maps:
elevation_vector_strength_3x3
elevation_fisher_1K_3x3
Calculations done.

(Tue Jan 12 10:41:00 2016) Command finished (1 min 18 sec)  

xml1.R

"WN_bat <- sub(".bat", "", 
list.files(paste(Sys.getenv("GISBASE"), "bin", sep="/"),
pattern=".bat$"))
if (nchar(Sys.getenv("GRASS_ADDON_BASE")) > 0) {
t0 <- try(sub(".bat", "", 
   list.files(paste(Sys.getenv("GRASS_ADDON_BASE"),
   "bin", sep="/"), pattern=".bat$")), silent=TRUE)
if (class(t0) != "try-error" && is.character(t0) &&
   nchar(t0) > 0)
   WN_bat <- c(WN_bat, t0)
assign("WN_bat", WN_bat, envir=.GRASS_CACHE)
}"

do it manually:

WN_bat <- sub(".bat", "", list.files(paste(Sys.getenv("GISBASE"), "bin",
sep="/"), pattern=".bat$"))
> WN_bat
  [1] "d.correlate"  "d.frame"  "d.out.file"
  [4] "d.polar"  "d.rast.edit"  "d.rast.leg"
  [7] "d.redraw" "d.shade"  "d.to.rast"
 [10] "d.what.rast"  "d.what.vect"  "db.dropcolumn"
 [13] "db.droptable" "db.in.ogr""db.out.ogr"
 [16] "db.test"  "db.univar""g.extension.all"
 [19] "g.extension"  "g.gui.animation"  "g.gui.datacatalog"
 [22] "g.gui.dbmgr"  "g.gui.gcp""g.gui.gmodeler"
 [25] "g.gui.iclass" "g.gui.mapswipe"   "g.gui.psmap"
 [28] "g.gui.rlisetup"   "g.gui.timeline"   "g.gui.tplot"
 [31] "g.gui.vdigit" "g.manual" "g.search.modules"
 [34] "i.colors.enhance" "i.image.mosaic"   "i.in.spotvgt"
 [37] "i.oif""i.pansharpen" "i.spectral"
 [40] "i.tasscap""m.proj"   "r.blend"
 [43] "r.buffer.lowmem"  "r.colors.stddev"  "r.fillnulls"
 [46] "r.grow"   "r.import" "r.in.aster"
 [49] "r.in.srtm""r.in.wms" "r.mask"
 [52] "r.out.xyz""r.pack"   "r.plane"
 [55] "r.reclass.area"   "r.rgb""r.shade"
 [58] "r.tileset""r.unpack" "r3.in.xyz"
 [61] "t.create" "t.info"   "t.list"
 [64] "t.merge"  "t.rast.accdetect" "t.rast.accumulate"
 [67] "t.rast.aggregate" "t.rast.aggregate.ds"  "t.rast.algebra"
 [70] "t.rast.colors""t.rast.contour"   "t.rast.export"
 [73] "t.rast.extract"   "t.rast.gapfill"   "t.rast.import"
 [76] "t.rast.list"  "t.rast.mapcalc"   "t.rast.neighbors"
 [79] "t.rast.out.vtk"   "t.rast.series""t.rast.to.rast3"
 [82] "t.rast.to.vect"   "t.rast.univar""t.rast.what"
 [85] "t.rast3d.algebra" "t.rast3d.extract" "t.rast3d.list"
 [88] "t.rast3d.mapcalc" "t.rast3d.univar"  "t.register"
 [91] "t.remove" "t.rename" "t.sample"
 [94] "t.select" "t.shift"  "t.snap"
 [97] "t.support""t.topology"   "t.unregister"
[100] "t.vect.algebra"   "t.vect.db.select" "t.vect.export"
[103] "t.vect.extract"   "t.vect.import""t.vect.list"
[106] "t.vect.observe.strds" "t.vect.univar""t.vect.what.strds"
[109] "v.build.all"  "v.centroids"  "v.db.addcolumn"
[112] "v.db.addtable""v.db.dropcolumn"  "v.db.droprow"
[115] "v.db.droptable"   "v.db.join""v.db.reconnect.all"
[118] "v.db.renamecolumn""v.db.univar"  "v.db.update"
[121] "v.dissolve"   "v.import" "v.in.e00"
[124] "v.in.geonames""v.in.lines"   "v.in.mapgen"
[127] "v.in.wfs" "v.krige"  "v.pack"
[130] "v.rast.stats" "v.report" "v.to.lines"
[133] "v.unpack" "v.what.strds" "v.what.vect"
[136] "wxpyimgview"
t0 <- sub(".bat", "", list.files(paste(Sys.getenv("GRASS_ADDON_BASE"),
"bin", sep="/"), pattern=".bat$"))
> t0
 [1] "m.ecad""r.basin"   "r.biodiversity"
 [4] "r.euroeco" "r.hypso"   "r.roughness.vector"
 [7] 

Re: [GRASS-stats] Using GRASS addons in R on Windows

[Helmut Kudrnovsky]

>
>Is %APPDATA% a predictable location on Windows? 

yes, %APPDATA% is predictable on Windows.

we set it e.g. in the winGRASS standalone installer here:

https://trac.osgeo.org/grass/browser/grass/branches/releasebranch_7_0/mswindows/GRASS-Installer.nsi.tmpl#L743
 

and on other places in the code.

>Where should I look to see where the correct values are stored on Unix
>(Linux and OSX?) and Windows? I see: GRASS_ADDON_BASE as GNU/Linux is
>$HOME/.grass7/addons, on MS Windows $APPDATA\GRASS7\addons in:
>
>https://grass.osgeo.org/grass70/manuals/variables.html

maybe some hints:

https://trac.osgeo.org/grass/browser/grass/branches/releasebranch_7_0/scripts/g.extension/g.extension.py#L1053





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Re: [GRASS-stats] Using GRASS addons in R on Windows

[Helmut Kudrnovsky]

>Thanks. I've committed changes to R-forge, which seem to work for me for
>Linux and Windows. The updated draft Windows binary is at:
>
>http://win-builder.r-project.org/KJJJkeazt7Sw/rgrass7_0.1-5.zip

> utils:::menuInstallLocal()
Paket ‘rgrass7’ erfolgreich ausgepackt und MD5 Summen abgeglichen
> 
> library(rgrass7)
Lade nötiges Paket: sp
Lade nötiges Paket: XML
GRASS GIS interface loaded with GRASS version: (GRASS not running)

from the https://cran.r-project.org/web/packages/rgrass7/rgrass7.pdf

Examples
## Not run:
initGRASS("/usr/bin/grass-7.0.0", home=tempdir())
initGRASS("C:/GRASS", home=tempdir())
## End(Not run)

as an used windows user I've tried first with Windows-typical backslash ;-)

initGRASS("C:\\Program Files\\GRASS GIS 7.1.svn", home=tempdir(),
gisDbase="C:\\grassdata", location="nc_spm_08", mapset="user1")

> initGRASS("C:\Program Files\GRASS GIS 7.1.svn", home=tempdir(),
> location="C:\grassdata\nc_spm_08\", mapset="user1")
Fehler: '\P' ist eine unbekannte Escape-Sequenz in der Zeichenkette
beginnend mit ""C:\P"
error: '\P' is an unkown escape sequence beginning with with ""C:\P"

then I tried double backslash

initGRASS("C:\\Program Files\\GRASS GIS 7.1.svn", home=tempdir(),
gisDbase="C:\\grassdata", location="nc_spm_08", mapset="user1")

> initGRASS("C:\\Program Files\\GRASS GIS 7.1.svn", home=tempdir(),
> gisDbase="C:\\grassdata", location="nc_spm_08", mapset="user1")
gisdbaseC:/grassdata 
locationnc_spm_08 
mapset  user1 
rows6 
columns 8 
north   222800 
south   222740 
west642590 
east642670 
nsres   10 
ewres   10 
projection  +proj=lcc +lat_1=36.16 +lat_2=34.34
+lat_0=33.75 +lon_0=-79 +x_0=609601.22 +y_0=0 +no_defs +a=6378137
+rf=298.257222101
+towgs84=0.000,0.000,0.000 +to_meter=1 

and the slash mentioned in the manual example

initGRASS("C:/Program Files/GRASS GIS 7.1.svn", home=tempdir(),
gisDbase="C:/grassdata", location="nc_spm_08", mapset="user1")

> initGRASS("C:/Program Files/GRASS GIS 7.1.svn", home=tempdir(),
> gisDbase="C:/grassdata", location="nc_spm_08", mapset="user1")
gisdbaseC:/grassdata 
locationnc_spm_08 
mapset  user1 
rows6 
columns 8 
north   222800 
south   222740 
west642590 
east642670 
nsres   10 
ewres   10 
projection  +proj=lcc +lat_1=36.16 +lat_2=34.34
+lat_0=33.75 +lon_0=-79 +x_0=609601.22 +y_0=0 +no_defs +a=6378137
+rf=298.257222101
+towgs84=0.000,0.000,0.000 +to_meter=1 

not sure what R's normal notation of MS windows paths are (slash or double
backslash), maybe an addition to the manual would be worth?

will testing winGRASS modules and addons later.



-
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Re: [GRASS-stats] Using GRASS addons in R on Windows

[Helmut Kudrnovsky]

>> library(rgrass7)
>> initGRASS("/usr/local/grass7", home=tempdir())
>sh: 1: g.gisenv: not found
>sh: 1: g.gisenv: not found
>sh: 1: g.gisenv: not found
>sh: 1: g.gisenv: not found
>sh: 1: g.gisenv: not found
>sh: 1: g.version: not found
>Error in system(paste("g.version", get("addEXE", envir = .GRASS_CACHE),  : 
>  error in running command

just a quick test on windows here:

> library(rgrass7)
Lade nötiges Paket: sp
Lade nötiges Paket: XML
GRASS GIS interface loaded with GRASS version: (GRASS not running)

> initGRASS("C:/Program Files/GRASS GIS 7.1.svn", home=tempdir())
gisdbaseC:/Users/x~1/AppData/Local/Temp/Rtmpk93Gnb 
locationfile55c44229c0 
mapset  file55c5711580b 
rows1 
columns 1 
north   1 
south   0 
west0 
east1 
nsres   1 
ewres   1 
projection  NA 

is your GRASS really living in /usr/local/grass7 ?



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Re: [GRASS-stats] initGRASS() never stops running?

[Helmut Kudrnovsky]

>I am using Rstudio within GRASS without problems (on Ubuntu 14.04). No
specific configuration required as >far as I remember. Also on Windows I
generally have no problem running Rstudio under GRASS (the latter >installed
using OSGeo4W), but there I had to define the path to Rstudio
(https://pvanb.wordpress.com
>/2014/12/17/access-r-from-grass-gis-on-windows/)

it shouldn't be needed anymore; some time ago I've added the path to R
studio to OSGeo4W- and standalone winGRASS 7, see:

https://trac.osgeo.org/grass/browser/grass/branches/releasebranch_7_0/mswindows/env.bat#L18
https://trac.osgeo.org/grass/browser/grass/branches/releasebranch_7_0/mswindows/osgeo4w/env.bat.tmpl#L18



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Re: [GRASS-stats] R 3.3.1 and GRASSGIS 7.0.4

[Helmut Kudrnovsky]

Anna Petrášová wrote
> On Thu, Jul 14, 2016 at 9:20 PM, Helmut Kudrnovsky 

> hellik@

>  wrote:
>>>When I enter the command echo %PATH% I get:
>>>[...]
>>>Dnvm\;C:\Program Files
>> (x86)\Skype\Phone\;c:\users\buer3379\appdata\local\enthought\canopy\user\scripts;C:\Users\buer3379\AppData\Local\Enthough\Canopy\User;C:\Users\buer3379\AppData\Local\Enthought\Canopy\User\Scripts;C:\Program
>> Files\RStudio\bin;C:\Program Files\R\R-3.3.1\bin\x64
>>
>> ok, R is in %PATH%
>>
>> the script works here on my win 10 machine out of the box.
>>
>> have you installed all the R packages needed by the GRASS addon?
>>
>>
>>
> 
> When you launch Rscript from GRASS terminal (the black one) what do you
> get?

Cleaning up temporary files...
Starting GRASS GIS...
WARNUNG: Sperren gleichzeitiger Zugriffe auf ein Mapset ist unter Windows
 nicht möglich.

  __  ___   _____
 / / __ \/   | / ___/ ___/   / /  _/ ___/
/ / __/ /_/ / /| | \__ \\_  \   / / __ / / \__ \
   / /_/ / _, _/ ___ |___/ /__/ /  / /_/ // / ___/ /
   \/_/ |_/_/  |_///   \/___///

Welcome to GRASS GIS 7.3.svn (r68855)
GRASS GIS homepage:  http://grass.osgeo.org
This version running through:Command Shell
(C:\Windows\system32\cmd.exe)
Help is available with the command:  g.manual -i
See the licence terms with:  g.version -c
See citation options with:   g.version -x
If required, restart the GUI with:   g.gui wxpython
When ready to quit enter:exit

Launching  GUI in the background, please wait...
Microsoft Windows [Version 10.0.10586]
(c) 2015 Microsoft Corporation. Alle Rechte vorbehalten.

C:\Users\hkmyr>Rscript
Usage: /path/to/Rscript [--options] [-e expr [-e expr2 ...] | file] [args]

--options accepted are
  --help  Print usage and exit
  --version   Print version and exit
  --verbose   Print information on progress
  --default-packages=list
  Where 'list' is a comma-separated set
of package names, or 'NULL'
or options to R, in addition to --slave --no-restore, such as
  --save  Do save workspace at the end of the session
  --no-environDon't read the site and user environment files
  --no-site-file  Don't read the site-wide Rprofile
  --no-init-file  Don't read the user R profile
  --restore   Do restore previously saved objects at startup
  --vanilla   Combine --no-save, --no-restore, --no-site-file
--no-init-file and --no-environ

'file' may contain spaces but not shell metacharacters
Expressions (one or more '-e ') may be used *instead* of 'file'
See also  ?Rscript  from within R




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Re: [GRASS-stats] R 3.3.1 and GRASSGIS 7.0.4

[Helmut Kudrnovsky]

>and start a normal windows console, just the one which is delivered by
windows itself and type RScript
>
>here on my side:
>
>Microsoft Windows [Version 10.0.10586]
>(c) 2015 Microsoft Corporation. Alle Rechte vorbehalten.
>
>C:\Users\>cd C:\Program Files\R\R-3.3.1\bin 

of course, first change to the R installation folder, see above



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Re: [GRASS-stats] R 3.3.1 and GRASSGIS 7.0.4

[Helmut Kudrnovsky]

>In order for GRASS to be able to find R executables, R must be on the
>PATH variable.

in the standalone winGRASS installer R is already in the %PATH% variable, so
no extra work is needed.

I hope I'll find some time to implement this also in OSGeo4W-winGRASS.

see in original report above, R is in %PATH% as R starts in the winGRASS
windows console.





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Re: [GRASS-stats] R 3.3.1 and GRASSGIS 7.0.4

[Helmut Kudrnovsky]

Anna Petrášová wrote
> Hi,
> 
> In order for GRASS to be able to find R executables, R must be on the
> PATH variable. Follow for example this solution:
> 
> https://pvanb.wordpress.com/2014/12/17/access-r-from-grass-gis-on-windows/
> 
> to make R accessible from GRASS permanently. A simple but temporary
> solution is to open GRASS GIS and paste the path to R in the black
> terminal:
> 
> set PATH=%PATH%;C:\Program Files\R\R-3.3.1\bin
> 
> but this has to be repeated after restarting GRASS session.
> 
> Anna
> 
> 
> 
> On Fri, Jul 1, 2016 at 4:19 PM, C. Buerger IV 

> cbuerger4@

>  wrote:
>> I'm attempting to use the FUTURES model for GRASSGIS, which requires an
>> interface with R to use the drudge function. I'm running Windows 7 and
>> the
>> automatic linkup between R and GRASS does not seem to be happening. When
>> working from the FUTURES package
>> I have run:
>>
>>  r.futures.potential -d input=sampling@practice1 output=potential.csv
>> columns=devpressure_0_5_92,slope,road_dens_perc,forest_1992_smooth_perc,dist_to_water_km,dist_to_protected_km,dist_interchanges_km,travel_time_cities
>> developed_column=urban_change_clip subregions_column=counties
>> min_variables=4 --overwrite
>>
>> and get:
>>
>> Running automatic model selection ...
>> Traceback (most recent call last):
>>   File "C:\Users\buer3379\AppData\Roaming\GRASS7\addons/scri
>> pts/r.futures.potential.py", line 185, in 
> 
>> sys.exit(main())
>>   File "C:\Users\buer3379\AppData\Roaming\GRASS7\addons/scri
>> pts/r.futures.potential.py", line 158, in main
>> stdout=subprocess.PIPE, stderr=subprocess.PIPE)
>>   File "C:\OSGEO4~1\apps\Python27\lib\subprocess.py", line
>> 711, in __init__
>> errread, errwrite)
>>   File "C:\OSGEO4~1\apps\Python27\lib\subprocess.py", line
>> 948, in _execute_child
>> startupinfo)
>> WindowsError: [Error 2] The system cannot find the file
>> specified
>>
>> In just attempting to run R via R--save I get:
>>
>> R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
>> Copyright (C) 2016 The R Foundation for Statistical Computing
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>   Natural language support but running in an English locale
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>> During startup - Warning messages:
>> 1: Setting LC_CTYPE=en_US.cp1252 failed
>> 2: Setting LC_COLLATE=en_US.cp1252 failed
>> 3: Setting LC_TIME=en_US.cp1252 failed
>> 4: Setting LC_MONETARY=en_US.cp1252 failed
>>>
>>
>> Does anyone have any pointers or tips to work around this problem.  Any
>> ideas would be appreicated.

just tested it now with standalone-winGRASS

System Info 
GRASS Version: 7.3.svn  
GRASS SVN revision: r68855  
Build date: 2016-07-06  
Build platform: x86_64-w64-mingw32  
GDAL: 2.0.2 
PROJ.4: 4.9.2   
GEOS: 3.5.0 
SQLite: 3.7.17  
Python: 2.7.5   
wxPython: 2.8.12.1  
Platform: Windows-8-6.2.9200

- without any change to %PATH%

- with the example from [1] (n.b. not exactly because too lazy and to tired
to follow all the exercises late at night)


r.futures.potential -d input=sampling output=potential.csv
columns=devpressure_0_5_92,slope,road_dens_perc,forest_1992_smooth_perc,dist_to_water_km,dist_to_protected_km,dist_interchanges_km,travel_time_cities
developed_column=urban_change_clip subregions_column=counties
min_variables=4
Running automatic model selection ...
Best model summary:
-
Beim Start - Warnmeldungen:
1: Setting LC_CTYPE=de_AT.cp1252 failed 
2: Setting LC_COLLATE=de_AT.cp1252 failed 
3: Setting LC_TIME=de_AT.cp1252 failed 
4: Setting LC_MONETARY=de_AT.cp1252 failed 
Fixed term is "(Intercept)"
Es gab 16 Warnungen (Anzeige mit warnings())
Generalized linear mixed model fit by maximum likelihood (Laplace
  Approximation) [glmerMod]
 Family: binomial  ( logit )
Formula: urban_change_clip ~ 

Re: [GRASS-stats] R 3.3.1 and GRASSGIS 7.0.4

[Helmut Kudrnovsky]

C. Buerger IV wrote
> I'm attempting to use the FUTURES
> https://grasswiki.osgeo.org/wiki/Workshop_on_urban_growth_modeling_with_FUTURES#Softwaremodel
> for GRASSGIS, which requires an interface with R to use the drudge
> function. I'm running Windows 7 and the automatic linkup between R and
> GRASS does not seem to be happening. When working from the FUTURES package
> I have run:
> 
>  r.futures.potential -d input=sampling@practice1 output=potential.csv
> columns=devpressure_0_5_92,slope,road_dens_perc,forest_1992_smooth_perc,dist_to_water_km,dist_to_protected_km,dist_interchanges_km,travel_time_cities
> developed_column=urban_change_clip subregions_column=counties
> min_variables=4 --overwrite
> 
> and get:
> 
> Running automatic model selection ...
> Traceback (most recent call last):
>   File "C:\Users\buer3379\AppData\Roaming\GRASS7\addons/scri
> pts/r.futures.potential.py", line 185, in 
> 
> sys.exit(main())
>   File "C:\Users\buer3379\AppData\Roaming\GRASS7\addons/scri
> pts/r.futures.potential.py", line 158, in main
> stdout=subprocess.PIPE, stderr=subprocess.PIPE)
>   File "C:\OSGEO4~1\apps\Python27\lib\subprocess.py", line
> 711, in __init__
> errread, errwrite)
>   File "C:\OSGEO4~1\apps\Python27\lib\subprocess.py", line
> 948, in _execute_child
> startupinfo)
> WindowsError: [Error 2] The system cannot find the file
> specified
> 
> In just attempting to run R via R--save I get:
> 
> R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
> Copyright (C) 2016 The R Foundation for Statistical Computing
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>   Natural language support but running in an English locale
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> During startup - Warning messages:
> 1: Setting LC_CTYPE=en_US.cp1252 failed
> 2: Setting LC_COLLATE=en_US.cp1252 failed
> 3: Setting LC_TIME=en_US.cp1252 failed
> 4: Setting LC_MONETARY=en_US.cp1252 failed
>>
> 
> Does anyone have any pointers or tips to work around this problem.  Any
> ideas would be appreicated.
> 
> C. L. Buerger IV

could you type in the winGRASS windows console:

echo %PATH%

?




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Re: [GRASS-stats] R 3.3.1 and GRASSGIS 7.0.4

[Helmut Kudrnovsky]

[please keep it on the ML]

>A Standalone install. At the time it seemed like what I wanted.

tested here:

System Info 
GRASS Version: 7.3.svn  
GRASS SVN revision: r68855  
Build date: 2016-07-06  
Build platform: x86_64-w64-mingw32  
GDAL: 2.0.2 
PROJ.4: 4.9.2   
GEOS: 3.5.0 
SQLite: 3.7.17  
Python: 2.7.5   
wxPython: 2.8.12.1  
Platform: Windows-8-6.2.9200 

typing R in the console:

Cleaning up temporary files...
Starting GRASS GIS...
WARNUNG: Sperren gleichzeitiger Zugriffe auf ein Mapset ist unter Windows
 nicht möglich.

  __  ___   _____
 / / __ \/   | / ___/ ___/   / /  _/ ___/
/ / __/ /_/ / /| | \__ \\_  \   / / __ / / \__ \
   / /_/ / _, _/ ___ |___/ /__/ /  / /_/ // / ___/ /
   \/_/ |_/_/  |_///   \/___///

Welcome to GRASS GIS 7.3.svn (r68855)
GRASS GIS homepage:  http://grass.osgeo.org
This version running through:Command Shell
(C:\Windows\system32\cmd.exe)
Help is available with the command:  g.manual -i
See the licence terms with:  g.version -c
See citation options with:   g.version -x
If required, restart the GUI with:   g.gui wxpython
When ready to quit enter:exit

Launching  GUI in the background, please wait...
Microsoft Windows [Version 10.0.10586]
(c) 2015 Microsoft Corporation. Alle Rechte vorbehalten.

C:\Users\>R

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

>I'm running Windows 7 and the automatic linkup between R and GRASS does not
seem to be happening. 

in the standalone R is in the %PATH% variable, so more investigation in the
r.future-script is needed.





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Re: [GRASS-stats] rgrass7 is not loading

[Helmut Kudrnovsky]

>Using Windows 7 Enterprise and R 3.3.0 and R 3.3.1, GRASS 7.0.4, and rgrass7
0.1-7 and 0.1-8, I see no >issues and cannot reproduce it. Could other users
of Windows (I am not a Windows user) please report >whether this loading
error is specific to the OP (and another person who contacted me offlist).
Do not >write to me offlist, only the list collectively is likely to resolve
this.

[snip]

> Error : .onAttach in attachNamespace() f├╝r 'rgrass7' fehlgeschlagen,
> Details:
>  Aufruf: if (class(t0) != "try-error" && is.character(t0) && nchar(t0) >
>  Fehler: Fehlender Wert, wo TRUE/FALSE n├Âtig ist 

looking at the error, it seems to come from:

https://r-forge.r-project.org/scm/viewvc.php/pkg/rgrass7/R/xml1.R?view=markup=spgrass

[...]
if (nchar(Sys.getenv("GRASS_ADDON_BASE")) > 0) {
t0 <- try(sub(".bat", "", 
   list.files(paste(Sys.getenv("GRASS_ADDON_BASE"),
   "bin", sep="/"), pattern=".bat$")), silent=TRUE)
if (class(t0) != "try-error" && is.character(t0) &&
   nchar(t0) > 0)
   WN_bat <- c(WN_bat, t0)
[...]

could it be that (some) addons raises this issue?








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Re: [GRASS-stats] rgrass7 is not loading

[Helmut Kudrnovsky]

[you have to be subscribed to post in this ML]


benhemingway wrote
> I am having the same problem. 
> 
> Windows 10 Home 64 bit. Native GRASS 7.0.4 R 3.3.1
> 
> When I try to load the rgrass7 library from within GRASS i get:
> 
> Error : .onAttach failed in attachNamespace() for 'rgrass7', details:
>   call: if (class(t0) != "try-error" && is.character(t0) && nchar(t0) >
>   error: missing value where TRUE/FALSE needed
> Error: package or namespace load failed for 'rgrass7'
> 
> When I try and load it from within R i get:
> 
> Loading required package: sp
> Loading required package: XML
> GRASS GIS interface loaded with GRASS version: (GRASS not running)
> 
> -Ben

after starting R in winGRASS and before library("rgrass7") , could you do: 

sessionInfo()

have you installed any GRASS addons? if yes, which one?

the addons are installed in C:\Users\yourusername\AppData\Roaming\GRASS7

if you have installed some GRASS addons, could you delete the addons folder
in the C:\Users\yourusername\AppData\Roaming\GRASS7

then restart winGRASS (without any addons installed) and R and try to do
library("rgrass7") again and report the results.





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Re: [GRASS-stats] GRASS GIS 7.0 (stable) and R integration issue

[Helmut Kudrnovsky]

>I've put a Windows binary and source of rgrass7_0.1-9 on:
>
>http://spatial.nhh.no/R/rgrass7/
>
>which I believe resolves the issue. Please test and report back (on list,
>subscribe first, then reply or post). Please also check with addons
>present to be sure that the fix works both with and without addons. 

tested here with:

System Info 
GRASS Version: 7.3.svn  
GRASS SVN revision: r69683  
Build date: 2016-10-07  
Build platform: x86_64-w64-mingw32  
GDAL: 2.1.1 
PROJ.4: 4.9.3   
GEOS: 3.5.0 
SQLite: 3.14.1  
Python: 2.7.5   
wxPython: 2.8.12.1  
Platform: Windows-8-6.2.9200 (OSGeo4W) 

-
with addons:

C:\>set PATH=%PATH%;"C:\Program Files\R\R-3.3.1\bin\x64"
C:\>R
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
[...]
> library("rgrass7")
Lade n├Âtiges Paket: sp
Lade n├Âtiges Paket: XML
GRASS GIS interface loaded with GRASS version: GRASS 7.3.svn (2016)
and location: nc_spm_08_grass7
[...]
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

locale:
[1] C

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

other attached packages:
[1] rgrass7_0.1-9 XML_3.98-1.4  sp_1.2-3

loaded via a namespace (and not attached):
[1] grid_3.3.1  lattice_0.20-34
[...]
> parseGRASS("r.flip")
Command: r.flip
Extension: .exe
Description: Flips an image.
Keywords: Flips an image.
Parameters:
  name: input, type: string, required: yes, multiple: no
  keydesc: name, keydesc_count: 1
[Name der Eingabe-Rasterkarte]
  name: output, type: string, required: yes, multiple: no
  keydesc: name, keydesc_count: 1
[Name der Ausgabe-Rasterkarte]
Flags:
  name: w [East-West flip] {FALSE}
  name: b [Both N-S and E-W flip] {FALSE}
  name: overwrite [Ausgabedateien d├╝rfen bereits existierende Dateien
├╝berschreiben.] {FALSE}
  name: help [Print usage summary] {FALSE}
  name: verbose [Ausf├╝hrlicher Ausgabemodus] {FALSE}
  name: quiet [Schweigsamer Ausgabemodus] {FALSE}
[...]
> parseGRASS("r.northerness.easterness")
Command: r.northerness.easterness
Extension: .bat
Description: Calculation of northerness, easterness and the interaction
between northerness and slope
Keywords: Raster, Gelände, aspect, slope, sun
Parameters:
  name: elevation, type: string, required: yes, multiple: no
  keydesc: name, keydesc_count: 1
[Name of elevation raster map]
Flags:
  name: help [Print usage summary] {FALSE}
  name: verbose [Ausf├╝hrlicher Ausgabemodus] {FALSE}
  name: quiet [Schweigsamer Ausgabemodus] {FALSE}

-  

without addons: 
  
C:\>set PATH=%PATH%;"C:\Program Files\R\R-3.3.1\bin\x64"
C:\>R
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
[...]
> library("rgrass7")
Lade n├Âtiges Paket: sp
Lade n├Âtiges Paket: XML
GRASS GIS interface loaded with GRASS version: GRASS 7.3.svn (2016)
and location: nc_spm_08_grass7
[...]
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

locale:
[1] C

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

other attached packages:
[1] rgrass7_0.1-9 XML_3.98-1.4  sp_1.2-3

loaded via a namespace (and not attached):
[1] grid_3.3.1  lattice_0.20-34
[...]
> parseGRASS("r.region")
Command: r.region
Extension: .exe
Description: Setzt die Begrenzungs-Definition (boundary) f├╝r eine
Rasterkarte.
Keywords: Raster, Metadaten
Parameters:
  name: map, type: string, required: yes, multiple: no
  keydesc: name, keydesc_count: 1
[Name of raster map to change]
  name: region, type: string, required: no, multiple: no
  keydesc: name, keydesc_count: 1
[Setze Region von benannter Region.]
  name: raster, type: string, required: no, multiple: no
  keydesc: name, keydesc_count: 1
[Setze Region angepasst an diese Rasterkarte.]
  name: vector, type: string, required: no, multiple: no
  keydesc: name, keydesc_count: 1
[Setze Region angepasst an diese Vektorkarte.]
  name: n, type: string, required: no, multiple: no
  keydesc: value, keydesc_count: 1
[Wert f├╝r die n├Ârdliche Grenze.]
  name: s, type: string, required: no, multiple: no
  keydesc: value, keydesc_count: 1
[Wert f├╝r die s├╝dliche Grenze.]
  name: e, type: string, required: no, multiple: no
  keydesc: value, 

Re: [GRASS-stats] rgrass7 is not loading

[Helmut Kudrnovsky]

>The OP replied off-list 20/9 that:
>
>"I'm working on win7 home professional.
>
>It's the latest r version (3.3.0) and native grass 7.0.4.
>
>The rgrass7 package is the latest, downloaded yesterday. In  the single r
session it works and reports that grass is not running.
>
>But if i start it in the grass session i get this error.
>
>It seems that there are any old grass r bindings which uses the namespaces
needed from the package.
>
>Until yesterday it worked fine...
>
>I searched for this issue, founded similar reports, but no solutions. Am"
>
>Using Windows 7 Enterprise and R 3.3.0 and R 3.3.1, GRASS 7.0.4, and
rgrass7 0.1-7 and 0.1-8, I see no issues and cannot reproduce it. Could
other users of Windows (I am not a Windows user) please report whether this
loading error is specific to the OP (and another person who contacted me
offlist). Do not write to me offlist, only the list collectively is likely
to resolve this. 

tested here on a win 10 64-bit box, and osgeo4w-winGRASS7.0.5; following
steps for testing:

- start a osgeo4w-winGRASS7.0.5-session

- adding R to %PATH%:

C:\>set PATH=%PATH%;"C:\Program Files\R\R-3.3.1\bin"

C:\>echo %PATH%
C:\OSGEO4~1\apps\grass\grass-7.0.5\lib;C:\OSGEO4~1\apps\grass\grass-7.0.5\bin;C:\Users\hkmyr\AppData\Roaming\GRASS7\addons\bin;C:\OSGEO4~1\apps\Python27\Scripts;C:\OSGEO4~1\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\WBem;C:\OSGEO4~1\apps\msys\bin;"C:\Program
Files\R\R-3.3.1\bin"

- following library versions are installed:

install.packages("sp") # sp_1.2-3
install.packages("rgdal") # rgdal_1.1-10
install.packages("rgrass7") # rgrass7_0.1-8

- then typing R in the osgeo4w-windows console:

C:\>R

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten.
Tippen Sie 'license()' or 'licence()' f├╝r Details dazu.

R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
Tippen Sie 'contributors()' f├╝r mehr Information und 'citation()',
um zu erfahren, wie R oder R packages in Publikationen zitiert werden
k├Ânnen.

Tippen Sie 'demo()' f├╝r einige Demos, 'help()' f├╝r on-line Hilfe, oder
'help.start()' f├╝r eine HTML Browserschnittstelle zur Hilfe.
Tippen Sie 'q()', um R zu verlassen.

Beim Start - Warnmeldungen:
1: Setting LC_CTYPE=de_AT.cp1252 failed
2: Setting LC_COLLATE=de_AT.cp1252 failed
3: Setting LC_TIME=de_AT.cp1252 failed
4: Setting LC_MONETARY=de_AT.cp1252 failed
>

- and loading rgrass7:

> library("rgrass7")
Lade n├Âtiges Paket: sp
Lade n├Âtiges Paket: XML
GRASS GIS interface loaded with GRASS version: GRASS 7.0.5 (2016)
and location: nc_spm_08_grass7

beside some locale setting issues,  library("rgrass7") works here on my
side.

I've tested it on a few 32bit/64bit win7/win8/win10-boxes, no issues so far
here in testing on my side.

taken from the mentioned error report:
> Error : .onAttach in attachNamespace() f├╝r 'rgrass7' fehlgeschlagen,
> Details:
>  Aufruf: if (class(t0) != "try-error" && is.character(t0) && nchar(t0) >
>  Fehler: Fehlender Wert, wo TRUE/FALSE n├Âtig ist 

what can be the reason of such an attachNamespace() issue?

two installed rgrass7 packages (with and without admin rights)?
locale issue?
path issue?

anything else to test?



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Re: [GRASS-stats] rgrass7 is not loading

[Helmut Kudrnovsky]

Helmut Kudrnovsky wrote
> what can be the reason of such an attachNamespace() issue?
> 
> two installed rgrass7 packages (with and without admin rights)?
> locale issue?
> path issue?
> 
> anything else to test?

maybe .Rprofile file that is loading it already at Startup?




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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

> >With the fix, R for Windows picks up the default personal library
location. 
>> This is both with Rgui started in the GRASS Layer Manager console, and in 
>> the Windows GRASS terminal. 
> >
>> Thanks very much!

>Excellent, thanks for the rapid test! Hence I'll backport the fix. 

thanks for testing and backporting. 

locally already working, I hope to find some time soon to implement that the
R-GRASS coupling in OSGEO4W-winGRASS works the same as in standalone
winGRASS. 



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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Helmut Kudrnovsky wrote
> if we let %HOME% untouched, the easiest way may be
> (similar as we already do it with Rstudio:
> IF EXIST "%ProgramFiles%\RStudio\bin\rstudio.exe" set
> PATH=%PATH%;%ProgramFiles%\RStudio\bin)
> 
> - check if there is C:\Users\yourusername\Documents\R
> - if yes, set R_USER=C:\Users\hkmyr\Documents
> 
> so the most common cases of private R libraries should be covered.
> 
> any comments/objections for this change?

after some testing on win7, win8, win10, I've committed:
https://lists.osgeo.org/pipermail/grass-commit/2016-November/040769.html

New Revision: 69883

Modified:
   grass/trunk/mswindows/env.bat
Log:
set R_USER if %USERPROFILE%\Documents\R\ exists to catch most common cases
of private R libraries in windows

it should catch at least the common cases where personal libraries are
located in %USERPROFILE%\Documents\R\ 

please test the next standalone winGRASS7.3.svn daily builds
(https://wingrass.fsv.cvut.cz/grass73/x86_64/ or
https://wingrass.fsv.cvut.cz/grass73/x86/).

if it works, it should be backported to the standalone winGRASS7.0.x and the
upcoming winGRASS7.2.



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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Helmut Kudrnovsky wrote
> 
> Helmut Kudrnovsky wrote
>> both changes should be discussed on the dev ML.
>> 
>> before such changes are implemented, the workaround to manage this issue
>> manually via the control panel should go to the wiki.
>> 
>> Anna, any suggestions?
> just opened a discussion on the dev ML:
> 
> https://lists.osgeo.org/pipermail/grass-dev/2016-November/083122.html

some insights regarding %HOME% in winGRASS:

https://lists.osgeo.org/pipermail/grass-dev/2016-November/083159.html

--
[GRASS-dev] does GRASS need HOME to be defined?
> >> anyone more insight, if %HOME% is needed in winGRASS?
> >
> >Done by Glynn in:
> >https://trac.osgeo.org/grass/changeset/37873
> 
> does GRASS need HOME to be defined?
> 
> any hints?

It's used G__home() on Unix (and as a fallback on Windows) and it's
used for G_rc_path() on Windows (for some reason, the Unix version
uses getpwuid(), which is probably incorrect in this context).

It may also be used implicitly by library functions or external
programs looking for configuration files.
--

https://lists.osgeo.org/pipermail/grass-stats/2016-November/001708.html
--
OK, so the extension would be to look in %HOME%/Documents to see if there 
is %HOME%/Documents/R, and if so do what? If R_LIBS_USER is set, do 
nothing, if not, set R_USER, or guess which win-library is the relevant 
one and set R_LIBS_USER? Even if this is redundant for non-R users?
--

so it's still to discuss what would be the best option to overcome this
issue.




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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Helmut Kudrnovsky wrote
> 
> Roger Bivand wrote
>> For me on Linux, R_LIBS is set by me and works, but on Windows the
>> default 
>> is (possibly) set in the Registry anyway, which would/should be used if 
>> R_LIBS is not set. Within R, .libPaths() should be the same inside GRASS 
>> and outside GRASS. In Linux I have chosen to set R_LIBS, in Windows 7, 
>> GRASS standalone 7.0.4, I can start R GUI in the GRASS GUI console
>> command 
>> line, and my personal library is found (no R_LIBS set, .libPaths()
>> returns 
>> the default). I haven't tried with GRASS 7.2 on Windows.
>  .libPaths() works here the same outside an inside a winGRASS session.
> everything works.
> 
> I've installed all my libraries system wide here, not to any personal
> folder like Anna.
> 
> so I'll test later by adding some libraries to a personal folder like
> Anna.

now tested by intalling some libraries into my personal library.

outside a winGRASS7.2.svn session

> .libPaths()
[1] "C:/Users/test/Documents/R/win-library/3.3"
[2] "C:/Program Files/R/R-3.3.1/library"
> 

inside a winGRASS7.2.svn session

> .libPaths()
[1] "C:/Program Files/R/R-3.3.1/library"

there is a diffference between inside and outside a winGRASS7.2.svn session



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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Helmut Kudrnovsky wrote
> now tested by intalling some libraries into my personal library.
> 
> outside a winGRASS7.2.svn session
> 
>> .libPaths()
> [1] "C:/Users/test/Documents/R/win-library/3.3"
> [2] "C:/Program Files/R/R-3.3.1/library"
>> 
> 
> inside a winGRASS7.2.svn session
> 
>> .libPaths()
> [1] "C:/Program Files/R/R-3.3.1/library"
> 
> there is a diffference between inside and outside a winGRASS7.2.svn
> session


now tested with standalone winGRASS7.0.5; same behaviour; inside a
winGRASS-session the personal library seems not to be found.

any idea?



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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Helmut Kudrnovsky wrote
> 
> Helmut Kudrnovsky wrote
>> now tested by intalling some libraries into my personal library.
>> 
>> outside a winGRASS7.2.svn session
>> 
>>> .libPaths()
>> [1] "C:/Users/test/Documents/R/win-library/3.3"
>> [2] "C:/Program Files/R/R-3.3.1/library"
>>> 
>> 
>> inside a winGRASS7.2.svn session
>> 
>>> .libPaths()
>> [1] "C:/Program Files/R/R-3.3.1/library"
>> 
>> there is a diffference between inside and outside a winGRASS7.2.svn
>> session
> now tested with standalone winGRASS7.0.5; same behaviour; inside a
> winGRASS-session the personal library seems not to be found.
> 
> any idea?

now changing into the locally GRASS source code where R-batch files lives
(D:\software_source\grass_trunk\mswindows\external\rbatch) and start R form
there (same mechanism as implemented in the standalone winGRASS):

D:\software_source\grass_trunk\mswindows\external\rbatch>R

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten.
Tippen Sie 'license()' or 'licence()' für Details dazu.

R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
Tippen Sie 'contributors()' für mehr Information und 'citation()',
um zu erfahren, wie R oder R packages in Publikationen zitiert werden
können.

Tippen Sie 'demo()' für einige Demos, 'help()' für on-line Hilfe, oder
'help.start()' für eine HTML Browserschnittstelle zur Hilfe.
Tippen Sie 'q()', um R zu verlassen.

> .libPaths()
[1] "C:/Users/test/Documents/R/win-library/3.3"
[2] "C:/Program Files/R/R-3.3.1/library"
>

here R finds both, the standard and the personal library.

so it seems winGRASS seems to hide the path to the personal library.




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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

>My Windows 7, GRASS 7.0.4 shows identical .libPaths() values both inside
>and out with RGui. I don't know how the location of the personal library
>folder is recorded - is it in the registry? How might one know? It looks
>like:
>
>Sys.getenv("R_LIBS_USER") 

tested within a winGRASS7.0.5 session:

> Sys.getenv("R_LIBS_USER")
[1] "C:\\Users\\test/R/win-library/3.3"
> .libPaths()
[1] "C:/Program Files/R/R-3.3.1/library"

R_LIBS_USER is listed there within the winGRASS session, but the path itself
looks odd.

outside a winGRASS7.0.5/7.2.svn session, everthing is ok with these
variables (see above).



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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Roger Bivand wrote
> On Tue, 15 Nov 2016, Anna Petrášová wrote:
> 
>> Hi,
>>
>> I installed latest R on fresh Windows 10, then I installed several
>> packages into my personal library, then I installed standalone GRASS
>> GIS 7.3, and when I run R from GRASS session, it does not see the
>> installed packages. .libPaths() called from GRASS session indeed does
>> not show the path to the personal library. I installed the packages
>> again in GRASS session and then it's OK. Any idea why this happens and
>> how to avoid that?
> 
> No idea, only you can reproduce what you are doing. Do you mean 7.3, the 
> development version? Try the 7.0 and 7.2 versions, and compare to see 
> which environment variables may not be being transferred (R_LIBS probably) 
> in GRASS 7.3. Are you running R in a Windows terminal (if such 
> exists in Windows 10) inside GRASS, or in the command line in the 
> GRASS GUI? If the latter, has this changed?

tested with winGRASS7.2.svn standalone installer

System Info 
GRASS version: 7.2.svn  
GRASS SVN revision: r69794  
Build date: 2016-11-13  
Build platform: x86_64-w64-mingw32  
GDAL: 2.1.2 
PROJ.4: 4.9.3   
GEOS: 3.5.0 
SQLite: 3.14.1  
Python: 2.7.5   
wxPython: 2.8.12.1  
Platform: Windows-8-6.2.9200   

in the winGRASS-provided windows console:

Cleaning up temporary files...
Starting GRASS GIS...
WARNING: Concurrent mapset locking is not supported on Windows

  __  ___   _____
 / / __ \/   | / ___/ ___/   / /  _/ ___/
/ / __/ /_/ / /| | \__ \\_  \   / / __ / / \__ \
   / /_/ / _, _/ ___ |___/ /__/ /  / /_/ // / ___/ /
   \/_/ |_/_/  |_///   \/___///

Welcome to GRASS GIS 7.2.svn (r69794)
GRASS GIS homepage:  http://grass.osgeo.org
This version running through:Command Shell
(C:\WINDOWS\system32\cmd.exe)
Help is available with the command:  g.manual -i
See the licence terms with:  g.version -c
See citation options with:   g.version -x
If required, restart the GUI with:   g.gui wxpython
When ready to quit enter:exit

Launching  GUI in the background, please wait...
Microsoft Windows [Version 10.0.14393]
(c) 2016 Microsoft Corporation. Alle Rechte vorbehalten.

C:\Users\test>R

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> q()
Save workspace image? [y/n/c]: n

C:\Users\test>echo %R_LIBS%
%R_LIBS%

I've implemented the R-winGRASS-connecting for the standalone installer by

https://trac.osgeo.org/grass/browser/grass/trunk/mswindows/external/rbatch
https://trac.osgeo.org/grass/browser/grass/trunk/mswindows/external/rbatch/R.bat

%R_LIBS% isn't listed there.




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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Helmut Kudrnovsky wrote
> both changes should be discussed on the dev ML.
> 
> before such changes are implemented, the workaround to manage this issue
> manually via the control panel should go to the wiki.
> 
> Anna, any suggestions?

just opened a discussion on the dev ML:

https://lists.osgeo.org/pipermail/grass-dev/2016-November/083122.html




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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Roger Bivand wrote
> Right. Both R and Python seem to use %USERPROFILE% which is predictably 
> present in modern Windows. In winGRASS this is used to set %HOME%, which R 
> uses instead of %USERPROFILE%. R believes a set %HOME%, leading to the 
> difficulties.

a list of available windows variables:

http://ss64.com/nt/syntax-variables.html

USERPROFILE:

%SystemDrive%\Users\{username}
This is equivalent to the $HOME environment variable in Unix/Linux 


Roger Bivand wrote
> Could the winGRASS startup set R_LIBS_USER itself, and free it on exit? If 
> the user had multiple /x.y library directories, the advice would be to set 
> manually in the control panel, if one, use that?

theoretically it would be possible to set R_LIBS_USER during installation; a
new logic has to be added to the nsis installer script.

the other way around may be to set %HOME% in winGRASS as
%USERPROFILE%\Documents.

both changes should be discussed on the dev ML.

before such changes are implemented, the workaround to manage this issue
manually via the control panel should go to the wiki.

Anna, any suggestions?




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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Roger Bivand wrote
> On Thu, 17 Nov 2016, Roger Bivand wrote:
> 
>> On Thu, 17 Nov 2016, Helmut Kudrnovsky wrote:
>>
>>> >  My Windows 7, GRASS 7.0.4 shows identical .libPaths() values both
>>> inside
>>> >  and out with RGui. I don't know how the location of the personal
>>> library
>>> >  folder is recorded - is it in the registry? How might one know? It
>>> looks
>>> >  like:
>>> > 
>>> >  Sys.getenv("R_LIBS_USER") 
>>>
>>>  tested within a winGRASS7.0.5 session:
>>> 
>>> >  Sys.getenv("R_LIBS_USER")
>>>  [1] "C:\\Users\\test/R/win-library/3.3"
>>> >  .libPaths()
>>>  [1] "C:/Program Files/R/R-3.3.1/library"
>>>
>>>  R_LIBS_USER is listed there within the winGRASS session, but the path
>>>  itself
>>>  looks odd.
>>
>> Unfortunately, I couldn't reproduce this with stand-alone GRASS 7.0.5 or
>> 7.2, 
>> Windows 7 Pro, R 3.3.2. I see the same .libPaths() values inside and
>> outside. 
>> But see below - I found out how to reproduce the problem predictably.
>>
>> The reason was (of course) that I'd forgotten that I had set R_LIBS_USER
>> in 
>> Control Panel -> System and Security -> System -> Advanced system
>> settings -> 
>> Environment Variables. I'd done this as a response to the extra work
>> caused 
>> at each annual change of the default address as R's version was
>> incremented. 
>> See also:
>>
>> https://stat.ethz.ch/R-manual/R-devel/library/base/html/libPaths.html
>>
>> So a workaround might to use the R_LIBS_USER environment variable in that 
>> setting, checking that the directory exists. R uses it internally as 
>> generated, but doesn't export it. I don't know how this plays
>> cross-platform.
> 
> In a context with Windows 7 without setting the R_LIBS_USER environment 
> variable, R outside GRASS reports:
> 
>> Sys.getenv("HOME")
> [1] "C:\\Users\\rsb\\Documents"
>> .libPaths()
> [1] "C:/Users/rsb/Documents/R/win-library/3.3"
> [2] "C:/Program Files/R/R-3.3.2/library"
> 
> but inside GRASS %HOME% is re-defined, so:
> 
>> Sys.getenv("HOME")
> [1] "C:\\Users\\rsb"
>> .libPaths()
> [1] "c:/Program Files/R/R-3.3.2/library"
> 
> as R cannot construct: subdirectory ‘R/win-library/x.y’ of the home 
> directory, for R x.y.z, because "C:\\Users\\rsb/R/win-library/x.y" does 
> not exist, and that is where R is looking (here in GRASS):
> 
>> Sys.getenv("R_LIBS_USER")
> [1] "C:\\Users\\rsb/R/win-library/3.3"
> 
> (the different dirseps do not matter).
> 
> Does WinGRASS need to change the HOME environment variable? If it does, 
> users of R in GRASS need to set R_LIBS or R_LIBS_USER, easiest once via 
> Control Panel.

could you download the files from
https://trac.osgeo.org/grass/browser/grass/trunk/mswindows/external/rbatch,
copy these to an arbitrary folder e.g. C:\wd\testfolder, open a windows
console within this folder and type R in the console, then try your test
with  Sys.getenv("R_LIBS_USER") and  .libPaths()?

for me it works that the general and private library is found by R.

I'll have a look if /where winGRASS changes %HOME%




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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Roger Bivand wrote
>> could you download the files from
>> https://trac.osgeo.org/grass/browser/grass/trunk/mswindows/external/rbatch,
>> copy these to an arbitrary folder e.g. C:\wd\testfolder, open a windows
>> console within this folder and type R in the console, then try your test
>> with  Sys.getenv("R_LIBS_USER") and  .libPaths()?
>>
>> for me it works that the general and private library is found by R.
> 
> OK, looks like this:
> 
>> Sys.getenv("R_LIBS_USER")
> [1] "C:\\Users\\rsb\\Documents/R/win-library/3.3"
>> .libPaths()
> [1] "C:/Users/rsb/Documents/R/win-library/3.3"
> [2] "C:/Program Files/R/R-3.3.2/library"
>> any(match(installed.packages()[,"Package"], "rgrass7"))
> [1] TRUE
> 
> But I don't see any recent revisions in that directory?


it is taken from https://github.com/ggrothendieck/batchfiles by author`s
permission.

so the script works outside a winGRASS session also for you.

but the same script doesn't work inside a winGRASS session. so it's maybe
related to some %HOME% issues as mentioned before.



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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Helmut Kudrnovsky wrote
> I had a look into the sources; I can't find a line of code where winGRASS
> changes %HOME% at the moment; but it obvious uses %USERPROFILE% as %HOME%. 

maybe just found it:

for trunk

https://trac.osgeo.org/grass/browser/grass/trunk/lib/init/grass.py#L712

712 def ensure_home():
713 """Set HOME if not set on MS Windows"""
714 if windows and not os.getenv('HOME'):
715 os.environ['HOME'] = os.path.join(os.getenv('HOMEDRIVE'),
716   os.getenv('HOMEPATH'))

and for the 7.0.x-line

https://trac.osgeo.org/grass/browser/grass/branches/releasebranch_7_0/lib/init/grass.py#L1338

1338# set HOME
1339if windows and not os.getenv('HOME'):
1340os.environ['HOME'] = os.path.join(os.getenv('HOMEDRIVE'),
1341  os.getenv('HOMEPATH'))




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Re: [GRASS-stats] GRASS can't find R packages from personal library on Windows

[Helmut Kudrnovsky]

Roger Bivand wrote
>>
>> no idea at the moment if this change in env.bat has a side effect to the
>> winGRASS installation; further tests are needed.
>>
> 
> See also
> 
>> ?"environment variables"
> 
> which on a Windows installation shows "R_USER" in the Windows specific 
> section at foot, this also loses /Documents within GRASS.

see my other mail where %HOME% is set by winGRASS-grass7xx.py

so it seems to be some kind of a "design mismatch" where eg. windows (via
%USERPROFILE) and python

C:\>python
Python 2.7.5 (default, May 15 2013, 22:44:16) [MSC v.1500 64 bit (AMD64)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import os
>>> os.getenv('HOME')
'C:\\Users\\hkmyr'
>>> os.getenv('HOMEPATH')
'\\Users\\hkmyr'
>>> os.getenv('HOMEDRIVE')
'C:'
>>>

and R looks for %HOME%.




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Re: [GRASS-stats] rgrass7 - SQLite and GML drivers not working for readVECT

[Helmut Kudrnovsky]

>Are SQLite and GML drivers disabled/broken in readVECT? I only get
driver="ESRI Shapefile" to work,

confirmed by:

---
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)

Matrix products: default

locale:
[1] C

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

other attached packages:
[1] rgrass7_0.1-9 XML_3.98-1.9  sp_1.2-5

loaded via a namespace (and not attached):
[1] compiler_3.4.0  rgdal_1.2-12grid_3.4.0  lattice_0.20-35
---

only driver="ESRI Shapefile" works here.

trying SQLite:

> bla5 <- readVECT("firestations", driver="SQLite")
Supported formats:
Error: driver %in% candDrivers is not TRUE



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Re: [GRASS-stats] rgrass7 - SQLite and GML drivers not working for readVECT

[Helmut Kudrnovsky]

>Are SQLite and GML drivers disabled/broken in readVECT? 

some earlier discussions I remembered:

https://lists.osgeo.org/pipermail/grass-stats/2015-July/001561.html
https://lists.osgeo.org/pipermail/grass-stats/2015-July/001562.html
[...]
https://lists.osgeo.org/pipermail/grass-stats/2015-June/date.html



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Re: [GRASS-stats] rgrass7 - SQLite and GML drivers not working for readVECT

[Helmut Kudrnovsky]

>For some vectors, I get the following warnings (loss of data apparently): 
>
>> bla2<-readVECT("census_wake2000")
>Exporting 105 areas (may take some time)...
>Warning 1: Value 120426752 of field AREA of feature 23 not successfully
written. Possibly due to too larger >number with respect to field width
>Warning 1: Value 108540592 of field AREA of feature 24 not successfully
written. Possibly due to too larger >number with respect to field width

it seems to be a shapefile/(ogr) issue, see:

v.out.ogr input=census_wake2000@PERMANENT
output=D:\wd\test\slkdf\census_wake2000.shp format=ESRI_Shapefile
Exporting 105 areas (may take some time)...
Warning 1: Value 120426752 of field AREA of feature 23 not
successfully written. Possibly due to too larger number with
respect to field width
Warning 1: Value 108540592 of field AREA of feature 24 not
successfully written. Possibly due to too larger number with
respect to field width
Warning 1: Value 136831232 of field AREA of feature 26 not
successfully written. Possibly due to too larger number with
respect to field width
Warning 1: Value 133581472 of field AREA of feature 37 not
successfully written. Possibly due to too larger number with
respect to field width
Warning 1: Value 186611808 of field AREA of feature 42 not
successfully written. Possibly due to too larger number with
respect to field width
Warning 1: Value 645046656 of field AREA of feature 43 not
successfully written. Possibly due to too larger number with
respect to field width
Warning 1: Value 550580288 of field AREA of feature 44 not
successfully written. Possibly due to too larger number with
respect to field width



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Re: [GRASS-stats] rgrass7 - SQLite and GML drivers not working for readVECT

[Helmut Kudrnovsky]

>> bla2<-readVECT("census_wake2000")
>Exporting 105 areas (may take some time)...
>Warning 1: Value 120426752 of field AREA of feature 23 not successfully
written. Possibly due to too larger >number with respect to field width

testing by:

v.out.ogr input=census_wake2000@PERMANENT
output=D:\wd\test\slkdf\census_wake2000.sqlite format=SQLite

D:\wd\test\slkdf>ogrinfo census_wake2000.sqlite
INFO: Open of `census_wake2000.sqlite'
  using driver `SQLite' successful.
1: census_wake2000 (Polygon)

D:\wd\test\slkdf>ogr2ogr test.shp census_wake2000.sqlite
Warning 1: Value 120426752 of field area of feature 23 not successfully
written. Possibly due to too larger number with respect to field width
Warning 1: Value 108540592 of field area of feature 24 not successfully
written. Possibly due to too larger number with respect to field width

the same warning as in readVect.

OTOH loading the test.shp in QGIS, it seems that the area value is
successfully written into the shapefile dbf attribute table. maybe worth to
ask in the GDAL ML for clarification for these warnings.



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Re: [GRASS-stats] rgrass7 - SQLite and GML drivers not working for readVECT

[Helmut Kudrnovsky]

>Von: "Roger Bivand" 
>Please report sessionInfo() in R, and check the ogrDrivers() list.

sessionInfo() already posted in the mail before, here again:

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)

Matrix products: default

locale:
[1] C

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

loaded via a namespace (and not attached):
[1] compiler_3.4.0

and

> ogrDrivers()
Error in ogrDrivers() : could not find function "ogrDrivers"
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Re: [GRASS-stats] rgrass7 - SQLite and GML drivers not working for readVECT

[Helmut Kudrnovsky]

 
 

Gesendet: Dienstag, 10. Oktober 2017 um 22:52 Uhr
Von: "Veronica Andreo" <veroand...@gmail.com>
An: "Roger Bivand" <roger.biv...@nhh.no>
Cc: "grass-stats@lists.osgeo.org" <grass-stats@lists.osgeo.org>, "Helmut 
Kudrnovsky" <hel...@web.de>
Betreff: Re: [GRASS-stats] rgrass7 - SQLite and GML drivers not working for 
readVECT

Hello Roger,
 Sorry I forgot this info. Here, the outputs:
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 26 (Twenty Six)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

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

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

loaded via a namespace (and not attached):
[1] compiler_3.4.1


> library(rgrass7)
Loading required package: sp
Loading required package: XML
GRASS GIS interface loaded with GRASS version: GRASS 7.3.svn (2017)
and location: nc_spm_08_grass7
> library(rgdal)
rgdal: version: 1.2-13, (SVN revision 686)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /usr/share/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-5
 
> ogrDrivers()
 name   long_name
1  AeronavFAA Aeronav FAA
2  AmigoCloud  AmigoCloud
3  ARCGEN   Arc/Info Generate
4  AVCBin    Arc/Info Binary Coverage
5  AVCE00   Arc/Info E00 (ASCII) Coverage
6 BNA   Atlas BNA
7   Carto   Carto
8    Cloudant  Cloudant / CouchDB
9 CouchDB  CouchDB / GeoCouch
10    CSV    Comma Separated Value (.csv)
11    CSW  OGC CSW (Catalog  Service for the Web)
12    DGN    Microstation DGN
13    DXF AutoCAD DXF
14 EDIGEO   French EDIGEO exchange format
15  ElasticSearch  Elastic Search
16 ESRI Shapefile  ESRI Shapefile
17 Geoconcept  Geoconcept
18    GeoJSON GeoJSON
19   Geomedia   Geomedia .mdb
20 GeoRSS  GeoRSS
21    GFT    Google Fusion Tables
22    GML Geography Markup Language (GML)
23   GPKG  GeoPackage
24   GPSBabel    GPSBabel
25  GPSTrackMaker   GPSTrackMaker
26    GPX GPX
27    HTF    Hydrographic Transfer Vector
28   HTTP   HTTP Fetching Wrapper
29 Idrisi    Idrisi Vector (.vct)
30 Interlis 1  Interlis 1
31 Interlis 2  Interlis 2
32    JML    OpenJUMP JML
33    JP2OpenJPEG  JPEG-2000 driver based on OpenJPEG library
34   JPEG2000 JPEG-2000 part 1 (ISO/IEC 15444-1), based on Jasper library
35    KML   Keyhole Markup Language (KML)
36 LIBKML    Keyhole Markup Language (LIBKML)
37   MapInfo File    MapInfo File
38 Memory  Memory
39   MSSQLSpatial   Microsoft SQL Server Spatial Database
40  MySQL   MySQL
41    NAS  

Re: [GRASS-stats] rgrass7 - SQLite and GML drivers not working for readVECT

[Helmut Kudrnovsky]

>Von: "Roger Bivand"
>And output of v.in.ogr -f?

v.in.ogr -f 
 JP2ECW (ro): ERDAS JPEG2000 (SDK 5.3)
 FileGDB (rw+): ESRI FileGDB
 PCIDSK (rw+): PCIDSK Database File
 netCDF (rw+): Network Common Data Format
 JP2OpenJPEG (rw): JPEG-2000 driver based on OpenJPEG library
 PDF (rw+): Geospatial PDF
 DB2ODBC (rw+): IBM DB2 Spatial Database
 ESRI Shapefile (rw+): ESRI Shapefile
 MapInfo File (rw+): MapInfo File
 UK .NTF (ro): UK .NTF
 OGR_SDTS (ro): SDTS
 S57 (rw+): IHO S-57 (ENC)
 DGN (rw+): Microstation DGN
 OGR_VRT (ro): VRT - Virtual Datasource
 REC (ro): EPIInfo .REC 
 Memory (rw+): Memory
 BNA (rw+): Atlas BNA
 CSV (rw+): Comma Separated Value (.csv)
 NAS (ro): NAS - ALKIS
 GML (rw+): Geography Markup Language (GML) <=
 GPX (rw+): GPX
 LIBKML (rw+): Keyhole Markup Language (LIBKML)
 KML (rw+): Keyhole Markup Language (KML)
 GeoJSON (rw+): GeoJSON
 Interlis 1 (rw+): Interlis 1
 Interlis 2 (rw+): Interlis 2
 OGR_GMT (rw+): GMT ASCII Vectors (.gmt)
 GPKG (rw+): GeoPackage
 SQLite (rw+): SQLite / Spatialite <=
 ODBC (rw+): ODBC
 WAsP (rw+): WAsP .map format
 PGeo (ro): ESRI Personal GeoDatabase
 MSSQLSpatial (rw+): Microsoft SQL Server Spatial Database
 OGR_OGDI (ro): OGDI Vectors (VPF, VMAP, DCW)
 PostgreSQL (rw+): PostgreSQL/PostGIS
 MySQL (rw+): MySQL
 OpenFileGDB (ro): ESRI FileGDB
 XPlane (ro): X-Plane/Flightgear aeronautical data
 DXF (rw+): AutoCAD DXF
 CAD (ro): AutoCAD Driver
 Geoconcept (rw+): Geoconcept
 GeoRSS (rw+): GeoRSS
 GPSTrackMaker (rw+): GPSTrackMaker
 VFK (ro): Czech Cadastral Exchange Data Format
 PGDUMP (rw+): PostgreSQL SQL dump
 OSM (ro): OpenStreetMap XML and PBF
 GPSBabel (rw+): GPSBabel
 SUA (ro): Tim Newport-Peace's Special Use Airspace Format
 OpenAir (ro): OpenAir
 OGR_PDS (ro): Planetary Data Systems TABLE
 WFS (ro): OGC WFS (Web Feature Service)
 HTF (ro): Hydrographic Transfer Vector
 AeronavFAA (ro): Aeronav FAA
 Geomedia (ro): Geomedia .mdb
 EDIGEO (ro): French EDIGEO exchange format
 GFT (rw+): Google Fusion Tables
 SVG (ro): Scalable Vector Graphics
 CouchDB (rw+): CouchDB / GeoCouch
 Cloudant (rw+): Cloudant / CouchDB
 Idrisi (ro): Idrisi Vector (.vct)
 ARCGEN (ro): Arc/Info Generate
 SEGUKOOA (ro): SEG-P1 / UKOOA P1/90
 SEGY (ro): SEG-Y
 XLS (ro): MS Excel format
 ODS (rw+): Open Document/ LibreOffice / OpenOffice Spreadsheet 
 XLSX (rw+): MS Office Open XML spreadsheet
 ElasticSearch (rw+): Elastic Search
 Walk (ro): Walk
 Carto (rw+): Carto
 AmigoCloud (rw+): AmigoCloud
 SXF (ro): Storage and eXchange Format
 Selafin (rw+): Selafin
 JML (rw+): OpenJUMP JML
 PLSCENES (ro): Planet Labs Scenes API
 CSW (ro): OGC CSW (Catalog  Service for the Web)
 VDV (rw+): VDV-451/VDV-452/INTREST Data Format
 GMLAS (rw): Geography Markup Language (GML) driven by application schemas
 TIGER (rw+): U.S. Census TIGER/Line
 AVCBin (ro): Arc/Info Binary Coverage
 AVCE00 (ro): Arc/Info E00 (ASCII) Coverage
 HTTP (ro): HTTP Fetching Wrapper
Supported formats:

---

both GML and SQLite there.

thanks for checking.

Helmut
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Re: [GRASS-stats] rgrass7 - SQLite and GML drivers not working for readVECT

[Helmut Kudrnovsky]

>Gesendet: Dienstag, 10. Oktober 2017 um 23:24 Uhr
>Von: "Ahmadou Dicko" <dicko.ahma...@gmail.com>
>An: "Helmut Kudrnovsky" <hel...@web.de>
>Cc: "Roger Bivand" <roger.biv...@nhh.no>, "grass-stats@lists.osgeo.org" 
><grass-stats@lists.osgeo.org>
>Betreff: Re: [GRASS-stats] rgrass7 - SQLite and GML drivers not working for 
>readVECT
>
>Hi everyone,
> 
>I think that using v.external -f (instead of v.in.ogr -f) can fix this issue 
>(didn't try yet)
> 
>
>execGRASS("v.external", flags = "f", intern = TRUE)
> [1] "ARCGEN"         "AVCBin"         "AVCE00"        
> [4] "AeronavFAA"     "AmigoCloud"     "BNA"           
> [7] "CAD"            "CSV"            "CSW"           
>[10] "Carto"          "Cloudant"       "CouchDB"       
>[13] "DGN"            "DXF"            "EDIGEO"        
>[16] "ESRI_Shapefile" "ElasticSearch"  "GFT"           
>[19] "GML"            "GPKG"           "GPSBabel"      
>[22] "GPSTrackMaker"  "GPX"            "GeoJSON"       
>[25] "GeoRSS"         "Geoconcept"     "Geomedia"      
>[28] "HTF"            "HTTP"           "Idrisi"        
>[31] "JML"            "JPEG2000"       "KML"           
>[34] "MSSQLSpatial"   "MapInfo_File"   "Memory"        
>[37] "MySQL"          "ODBC"           "ODS"           
>[40] "OGR_GMT"        "OGR_GRASS"      "OGR_PDS"       
>[43] "OGR_SDTS"       "OGR_VRT"        "OSM"           
>[46] "OpenAir"        "OpenFileGDB"    "PCIDSK"        
>[49] "PDF"            "PGDUMP"         "PGeo"          
>[52] "PLSCENES"       "PostgreSQL"     "REC" 
 
in a quick check, there is no difference in available formats.
 
 
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Re: [GRASS-stats] R and GRASS on Windows - Status 1

[Helmut Kudrnovsky]

Maximilian Bakenhus wrote
> Hello all,
> 
> nearly any GRASS command which I write gives me Errors like:
> 
> 1: running command 'r.to.vect.exe --quiet --overwrite input=sites_catchm_1
> output=sites_catchm_1_v type=area' had status 1
> 
> 2: running command 'v.overlay.exe --overwrite --quiet
> ainput=veg_01_sa_31467.shp binput=sites_catchm_1_v operator=and
> output=veg_01_sa_31467.shp_1 olayer=1,0,0' had status 1
> 
> 3: running command 'v.db.addcolumn.bat map=veg_01_sa_31467.shp_1
> columns="area double precision"' had status 1
> 
> I guess this is because of wrong permissions ?
> How can I get along with that ?

(1) which R version?
(2) which GRASS version? standalone wingrass or OSGeo4W wingrass?
(3) how is the exact command in R?



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Re: [GRASS-stats] R and GRASS on Windows - Status 1

[Helmut Kudrnovsky]

---
(1)‘3.4.2’of R, Version 1.1.383   of R Studio
(2) GRASS Standalone
(3) 
 

a <- NULL
for(i in 1:length(anames)){
  print(anames[i])
  a <- c(a,unique(execGRASS("v.db.select", 
parameters = list(
  map = anames[i],
  columns = "objart"
), intern = T)[-1]))
}
 

Warning messages:
1: running command 'v.db.select.exe map=veg_01_sa_31467.shp columns=objart'
had status 1
 

 

 

For any GRASS related command I get a similar error.
 

you have to keep it on the mailing list, otherwise no one is able to answer.



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Re: [GRASS-stats] rgrass7 - SQLite and GML drivers not working for readVECT

[Helmut Kudrnovsky]

>Please try:
>
>install.packages("rgrass7", repos="http://R-Forge.R-project.org;)
>
>which incorporates the change in both places, not just one as before (svn
>revision 63 on R-Forge, spgrass project). 

tested with above install.packages cmd:

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)

Matrix products: default

locale:
[1] C

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

other attached packages:
[1] rgrass7_0.1-11 XML_3.98-1.9   sp_1.2-5

loaded via a namespace (and not attached):
[1] compiler_3.4.0  grid_3.4.0  lattice_0.20-35
>

it works here on winGRASS.



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Re: [GRASS-stats] error when trying to start GRASS from Rstudio in Windows

[Helmut Kudrnovsky]

Veronica Andreo wrote
> Hi
> 
> I taught a GRASS course last week and all students got the same error when
> trying to init GRASS from R or Rstudio (in all cases grass was installed
> through OSGeo4W installer).
> 
> Here´s the command we used (paths must be adapted accordingly):
> 
> initGRASS(gisBase = "C:/OSGeo4W64/apps/grass/grass-7.4.2RC2",
>   gisDbase = "C:/Users/RETA/Documents/grassdata",
>   location = "nc_spm_08_grass7",
>   mapset = "user1",
>   SG = "elevation")
> 
> The pop-up error is a missing iconv.dll. See screenshot attached. I
> believe
> all locales were in Spanish as well as the laptop I am testing now. After
> many attempts to try to close the pop-up error, we got the following in
> the
> Rstudio console:
> 
> Error in if (!compatible) { : argument is of length zeroIn addition:
> Warning messages:1: In system(paste("g.dirseps.exe -g",
> shQuote(Sys.getenv("GISRC"))),  :  running command 'g.dirseps.exe -g
> "junk"' had status 3092: In system(paste("g.dirseps.exe -g",
> shQuote(gisDbase)), intern = TRUE) :  running command 'g.dirseps.exe
> -g "C:/Users/RETA/Documents/grassdata"' had status 3093: In
> dir.create(loc_path) :  cannot create dir 'NA\nc_spm_08_grass7',
> reason 'No such file or directory'4: In dir.create(paste(loc_path,
> "PERMANENT", sep = "/")) :  cannot create dir
> 'NA\nc_spm_08_grass7\PERMANENT', reason 'No such file or directory'5:
> In dir.create(paste(loc_path, mapset, sep = "/")) :  cannot create dir
> 'NA\nc_spm_08_grass7\user1', reason 'No such file or directory'6: In
> system(paste("g.version", get("addEXE", envir = .GRASS_CACHE),  :
> running command 'g.version.exe' had status 309
> 
> Is this grass or windows problem? I did not get this error in this same
> laptop a month ago when Roger fixed some other problems. Seems that
> something changed meanwhile.

tested here now with


System Info 
GRASS version: 7.4.2
GRASS SVN revision: r73591  
Build date: 2018-10-23  
Build platform: x86_64-w64-mingw32  
GDAL: 2.3.2 
PROJ.4: 5.2.0   
GEOS: 3.7.0 
SQLite: 3.17.0  
Python: 2.7.14  
wxPython: 2.8.12.1  
Platform: Windows-10-10.0.17134 (OSGeo4W) 
-


 > sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

l
[1] LC_COLLATE=German_Austria.1252  LC_CTYPE=German_Austria.1252   
LC_MONETARY=German_Austria.1252 LC_NUMERIC=C   
LC_TIME=German_Austria.1252

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

other attached packages:
[1] rgrass7_0.1-10 XML_3.98-1.11  sp_1.3-1  

loaded via a namespace (and not attached):
[1] compiler_3.4.4  grid_3.4.4  lattice_0.20-35
  
- 

confirmed, also here a iconv.dll-issue (missing iconv.dll); and also
confirmed that it worked a month or so ago.

closer look at the error message and the used dependencies:

winGRASS 7.4.2 is now compiled against GDAL: 2.3.2 and PROJ.4: 5.2.0

when I tried a month or so ago, winGRASS was compiled against GDAL 2.0.X (or
similar) and PROJ.4 4.9. (or similar).

it seems there could be a dll mismatch between old and new dependencies
versions; hence the iconv.dll issue.
 






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Re: [GRASS-stats] error when trying to start GRASS from Rstudio in Windows

[Helmut Kudrnovsky]

>I got the same error a while back and I ended up finding a workaround by
copying all of the .dll files from >C:\OSGeo4W64\bin to
C:\OSGeo4W64\apps\grass\grass-7.4.1\bin. I have grass installed on my C
drive >but follow the path to your installation path bin. It appears that
the .dlls are different or incompatible.

yes, it is a dll mismatch. please report this in the GRASS ML, or better
open a ticket about this in the bugtracker



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Re: [GRASS-stats] error when trying to start GRASS from Rstudio in Windows

[Helmut Kudrnovsky]

Markus Neteler wrote
> On Thu, Nov 1, 2018 at 1:20 PM Veronica Andreo 

> veroandreo@

>  wrote:
>> In the body of the ticket I mentioned that the "pop-up error is a missing
>> iconv.dll" and
> 
> Yes - but the real error message might help.

see https://lists.osgeo.org/pipermail/grass-dev/2018-November/090433.html
for the solution:

"starting R/RGUi/RStudio from the OSGeo4W-console, then it works."




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Re: [GRASS-stats] Error when starting grass from R (grass installed thru osgeo4w)

[Helmut Kudrnovsky]

>How to find/test for the location of PROJ shared files?

see

https://r-forge.r-project.org/scm/viewvc.php/pkg/rgrass7/R/initGRASS.R?root=spgrass=55=64

for a diff



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Re: [GRASS-stats] Error when starting grass from R (grass installed thru osgeo4w)

[Helmut Kudrnovsky]

>I could reproduce the problem after starting the OSGeo4W console from the
>desktop shortcut icon.
>
>The problem seems to be that OSGeo4W's console starts in a directory for
>which the user does not have write access (for me from a desktop shortcut
>C:\Users\Public\Desktop\OSGeo4W). Because rgrass7::initGRASS() needs to
>write a GISRC file in the working directory, it needs write access. When I
>changed working directory to one to which I did have write access, the
>current CRAN binary rgrass7 loaded correctly under OSGeo4W for a
>throw-away location. I haven't yet tried with a pre-existing location.
>
>Could you check and see whether this seems reasonable?
>
>If so, I'll add a check for write access in the working directory to give
>a more sensible error message.

tested here with an existing location while changed the working directory to
writable directory:

--
run o-help for a list of available commands
C:\>d:

D:\>cd temp

D:\temp>cd testR

D:\temp\testR>R

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten.
Tippen Sie 'license()' or 'licence()' für Details dazu.

R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
Tippen Sie 'contributors()' für mehr Information und 'citation()',
um zu erfahren, wie R oder R packages in Publikationen zitiert werden
können.

Tippen Sie 'demo()' für einige Demos, 'help()' für on-line Hilfe, oder
'help.start()' für eine HTML Browserschnittstelle zur Hilfe.
Tippen Sie 'q()', um R zu verlassen.

> library(rgrass7)
Lade nötiges Paket: sp
Lade nötiges Paket: XML
GRASS GIS interface loaded with GRASS version: (GRASS not running)
> initGRASS(gisBase = "C:/OSGeo4W64/apps/grass/grass-7.4.1",
+ gisDbase = "D:/grassdata/", location = "nc_spm_08_grass7",
+ mapset = "user1", SG="elevation")
gisdbaseD:/grassdata/
locationnc_spm_08_grass7
mapset  user1
rows474
columns 526
north   228527.2
south   215018.2
west629980
east644971
nsres   28.5
ewres   28.5
projection  +proj=lcc +lat_1=36.16 +lat_2=34.34
+lat_0=33.75 +lon_0=-79 +x_0=609601.22 +y_0=0 +no_defs +a=6378137
+rf=298.257222101 +towgs84=0.000,0.000,0.000 +to_meter=1
Warnmeldung:
In dir.create(gisDbase) : 'D:\grassdata' existiert bereits
> g <- gmeta()
> g
gisdbaseD:/grassdata/
locationnc_spm_08_grass7
mapset  user1
rows474
columns 526
north   228527.2
south   215018.2
west629980
east644971
nsres   28.5
ewres   28.5
projection  +proj=lcc +lat_1=36.16 +lat_2=34.34
+lat_0=33.75 +lon_0=-79 +x_0=609601.22 +y_0=0 +no_defs +a=6378137
+rf=298.257222101 +towgs84=0.000,0.000,0.000 +to_meter=1
>
-

yes, the issue is that OSGeo4W's console starts in a directory for
which the user does not have write access.

changing to a directory with write access starting grass from R works as
expected.

I'll change the wiki accordingly.

>If so, I'll add a check for write access in the working directory to give
>a more sensible error message.

that would be helpful.




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Re: [GRASS-stats] Error when starting grass from R (grass installed thru osgeo4w)

[Helmut Kudrnovsky]

Roger Bivand wrote
> Note that rgrass7 has not been tested on OSGeo4W for many years, so the
> logic differences from Windows may no longer hold. Using Live has often
> been a better choice, but as I never use QGIS, I've no experience. Reports
> on issues with OSGei4W welcome.
> 
> Roger
> 
> Roger Bivand
> Norwegian School of Economics
> Bergen, Norway
> 
> 
> 
> Fra: Helmut Kudrnovsky
> Sendt: søndag 16. september, 16.26
> Emne: Re: [GRASS-stats] Error when starting grass from R (grass
> installedthru osgeo4w)
> Til: 

> grass-stats@.osgeo

> 
> 
> Veronica Andreo wrote > Hello, > > I am preparing a one week GRASS GIS
> course and I mostly expect Windows > users, so I recommend to install from
> OSGeo4W that allows to easily > install > also QGIS, msys (to get nice
> bash tricks) and other libraries that are > then > needed for some grass
> add-ons. > > The last day of the course, I'll show the connection with R.
> Now, starting > R within a grass session works as expected. But I get
> errors when trying > to > initialize GRASS (installed from OSGeo4W) from R
> console. I am following > the instructions in the wiki [0] > > First, I
> had to change the slashes from windows type, to linux type > (because I
> got: > Error: '\O' in an unrecognized escape in character string ""C:\O").
> > > After that, I get the following: > >> initGRASS(gisBase =
> 'C:/OSGeo4W64/apps/grass/grass-7.4.0', gisDbase = >
> 'C:/Users/RETA/Documents/grassdata', location = 'nc_spm_08_grass7', mapset
> > = 'user1', SG='elevation') > Error in if (!compatible) { : argumento
> tiene longitud cero > Además: Warning messages: > 1: In
> system(paste("g.dirseps.exe -g", shQuote(Sys.getenv("GISRC"))), : >
> comando ejecutado 'g.dirseps.exe -g "junk"' tiene estatus 309 > 2: In
> system(paste("g.dirseps.exe -g", shQuote(gisDbase)), intern = TRUE) > : >
> comando ejecutado 'g.dirseps.exe -g "C:/Users/RETA/Documents/grassdata"' >
> tiene estatus 309 > 3: In dir.create(loc_path) : > cannot create dir
> 'NA\nc_spm_08_grass7', reason 'No such file or > directory' > 4: In
> dir.create(paste(loc_path, "PERMANENT", sep = "/")) : > cannot create dir
> 'NA\nc_spm_08_grass7\PERMANENT', reason 'No such file or > directory' > 5:
> In dir.create(paste(loc_path, mapset, sep = "/")) : > cannot create dir
> 'NA\nc_spm_08_grass7\user1', reason 'No such file or > directory' > 6: In
> system(paste("g.version", get("addEXE", envir = .GRASS_CACHE), : > comando
> ejecutado 'g.version.exe' tiene estatus 309 > > Any hints? I also attach a
> screenshot with the message that appears (I > cannot copy/paste the text
> in that message) > > Thanks much in advance! > Vero > > [0]
> https://grasswiki.osgeo.org/wiki/R_statistics/rgrass7#GRASS_within_R > >
> ___ > grass-stats mailing list
> > grass-stats@.osgeo >
> https://lists.osgeo.org/mailman/listinfo/grass-stats > >
> Rgui_2018-09-13_22-19-45.png (73K) >
> http://osgeo-org.1560.x6.nabble.com/attachment/5378245/0/Rgui_2018-09-13_22-19-45.png;
> it's a missing dll. Are you invoking R from inside the OSGeo4W command
> console? - best regards Helmut -- Sent from:
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> 
> 
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Working for years now winGRASS-R only in OSGeo4w, I would call it well
tested.



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Re: [GRASS-stats] Error when starting grass from R (grass installed thru osgeo4w)

[Helmut Kudrnovsky]

>Should I open R from OSGeo4W command console and then init grass there? Is
that the workflow?

Yes, that's the workflow.

because environment variables for e.g. gdal, proj4 etc have to be set. And
that's nicely done in the OSGeo4W command line



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Re: [GRASS-stats] Error when starting grass from R (grass installed thru osgeo4w)

[Helmut Kudrnovsky]

Veronica Andreo wrote
> Hello,
> 
> I am preparing a one week GRASS GIS course and I mostly expect Windows
> users, so I recommend to install from OSGeo4W that allows to easily
> install
> also QGIS, msys (to get nice bash tricks) and other libraries that are
> then
> needed for some grass add-ons.
> 
> The last day of the course, I'll show the connection with R. Now, starting
> R within a grass session works as expected. But I get errors when trying
> to
> initialize GRASS (installed from OSGeo4W) from R console. I am following
> the instructions in the wiki [0]
> 
> First, I had to change the slashes from windows type, to linux type
> (because I got:
> Error: '\O' in an unrecognized escape in character string ""C:\O").
> 
> After that, I get the following:
> 
>> initGRASS(gisBase = 'C:/OSGeo4W64/apps/grass/grass-7.4.0', gisDbase =
> 'C:/Users/RETA/Documents/grassdata', location = 'nc_spm_08_grass7', mapset
> = 'user1', SG='elevation')
> Error in if (!compatible) { : argumento tiene longitud cero
> Además: Warning messages:
> 1: In system(paste("g.dirseps.exe -g", shQuote(Sys.getenv("GISRC"))), :
> comando ejecutado 'g.dirseps.exe -g "junk"' tiene estatus 309
> 2: In system(paste("g.dirseps.exe -g", shQuote(gisDbase)), intern = TRUE)
> :
> comando ejecutado 'g.dirseps.exe -g "C:/Users/RETA/Documents/grassdata"'
> tiene estatus 309
> 3: In dir.create(loc_path) :
> cannot create dir 'NA\nc_spm_08_grass7', reason 'No such file or
> directory'
> 4: In dir.create(paste(loc_path, "PERMANENT", sep = "/")) :
> cannot create dir 'NA\nc_spm_08_grass7\PERMANENT', reason 'No such file or
> directory'
> 5: In dir.create(paste(loc_path, mapset, sep = "/")) :
> cannot create dir 'NA\nc_spm_08_grass7\user1', reason 'No such file or
> directory'
> 6: In system(paste("g.version", get("addEXE", envir = .GRASS_CACHE), :
> comando ejecutado 'g.version.exe' tiene estatus 309
> 
> Any hints? I also attach a screenshot with the message that appears (I
> cannot copy/paste the text in that message)
> 
> Thanks much in advance!
> Vero
> 
> [0] https://grasswiki.osgeo.org/wiki/R_statistics/rgrass7#GRASS_within_R
> 
> ___
> grass-stats mailing list

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> https://lists.osgeo.org/mailman/listinfo/grass-stats
> 
> Rgui_2018-09-13_22-19-45.png (73K)
> http://osgeo-org.1560.x6.nabble.com/attachment/5378245/0/Rgui_2018-09-13_22-19-45.png;

it's a missing dll.

Are you invoking R from inside the OSGeo4W command console?



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Re: [GRASS-stats] Error when starting grass from R (grass installed thru osgeo4w)

[Helmut Kudrnovsky]

>OK, thanks for confirming that OSGeo4W remains feasible for rgrass7; I don't
have access. Does usability >include initGRASS()? This would be most fragile
because environment variables are being set, and >condition on Windows and
OSGeo4W.

R within a GRASS session works quite well so far.

did a fresh svn up of 

svn://r-forge.r-project.org/svnroot/spgrass

and quickly screened pkg\rgrass7\R\initGRASS.R:

e.g.

Sys.setenv(GRASS_PROJSHARE=paste(Sys.getenv("GISBASE"),
"\\proj", sep=""))

AFAIK at least the GRASS7.4.x line doesn't use anymore an own copy of the
PROJSHARE files; instead it uses the PROJ files itself; that's for all
platforms (linux, MacOS, MS Windows, ...).

e.g. in OSGeo4W 64bit it's defined as:

SET OSGEO4W_ROOT=C:\OSGeo4W64
set GRASS_PROJSHARE=%OSGEO4W_ROOT%\share\proj

only in the standalone installer, it's still defined as:

set GRASS_PROJSHARE=%GISBASE%\share\proj

because it's bundled in the installer.

e.g.

Sys.setenv(PATH=paste(Sys.getenv("GISBASE"), "\\extrabin;",
Sys.getenv("PATH"), sep=""))

there is no C:\OSGeo4W64\apps\grass\grass-7.4.1, because all of the
dependencies etc are living e.g. in 
C:\OSGeo4W64\bin, C:\OSGeo4W64\lib, ...

I'm not sure about this one:

[...]
Sys.setenv(GISBASE=gisBase)
if (missing(home)) home <- Sys.getenv("USERPROFILE")
[...]
Sys.setenv(GISRC=paste(Sys.getenv("HOME"), "\\.grassrc7", sep=""))

in winGRASS (standalone, OSGeo4W), the rc file lives in
C:\Users\YourUserName\AppData\Roaming\GRASS7 and not in %USERPROFILE%

and it seems around these lines:

[...]
Sys.setenv(GISRC="junk")
cat("GISDBASE:", getwd(), "\n", file=Sys.getenv("GISRC"))
cat("LOCATION_NAME: ", "\n", file=Sys.getenv("GISRC"),
append=TRUE)
cat("MAPSET: ", "\n", file=Sys.getenv("GISRC"),
append=TRUE)
gisrc <- ifelse (use_g.dirseps.exe, system(paste("g.dirseps.exe -g",
shQuote(Sys.getenv("GISRC"))), intern=TRUE),
Sys.getenv("GISRC"))
[...]

initGRASS gets in trouble in OSGeo4W.



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Re: [GRASS-stats] Package rgrass7 - g.extension function

[Helmut Kudrnovsky]

romain Fer. wrote
> Hello,
> 
> I am a french student in master's degrees, in advence I'm sorry for my
> english.
> 
> I using the package rgrass7 with R during my internship and I have a error
> on one function of this package. I use g.extension to import r.clip. I
> explain this error on this forum :
> https://gis.stackexchange.com/questions/360310/install-grass-extension-with-g-extension-and-rstudio
> 
> Can you look my explications of this problem and do you give me your
> opinion on this error ?
> 
> Thanks you in advance for your help,

there are maybe several issues here:

>initGRASS("C:/Program Files/GRASS GIS 7.6"

is it possible to upgrade to the 7.8.x-line?

>libgis_revison = grass.version()['libgis_revision']
>KeyError: 'libgis_revision'

AFAIR there have been some issues with libgis_revision in earlier versions;
this should be addressed in 7.8.x-line.

>ATTENTION: GRASS_ADDON_BASE is not defined

this variable should be defined that the addon is installed in the correst
place.

when you use winGRASS out of RStudio, are there all needed variables
defined?

see 

https://github.com/OSGeo/grass/blob/master/mswindows/env.bat 

for hints which variables should be defined in minimum that standalone
winGRASS is working.

%GISBASE% is the installation path to standalone winGRASS.




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