initGRASS versus R in grass - WAS: [GRASS-stats] Error using GRASS from R

[Rainer M Krug]

On Thu, Jul 21, 2011 at 10:52 AM, Rainer M Krug <r.m.krug at gmail.com> wrote:

>
>
> 2011/7/20 Roger Bivand <Roger.Bivand at nhh.no>
>
>> On Wed, 20 Jul 2011, Tim Besser wrote:
>>
>>  Dear GRASS-community,
>>>
>>> I have a very strange problem. I wrote a script in R (2.10.1) for the
>>> preparation of my datasets which works fine on my laptop (winxp). I do not
>>> start my R session from GRASS but use GRASS through the initGRASS and
>>> execGRASS commands. I use the "spgrass6" package and GRASS 6.4.1. As the
>>> script would run for days on my old laptop I now got a remote desktop
>>> connection to a much faster computer at the university (win7). However,
>>> while cmds like r.reclass or r.in.gdal (execGRASS) work on that computer the
>>> r.patch (execGRASS) cmd produces following error:
>>>
>>
>> Do not start R in GRASS using initGRASS when you are using an exiting
>> location - I will most likely remove this possibility at the next release as
>> it confuses users
>
>
> No - please don't. I am using it a lot, and it works very nicely (at least
> (and only?) for me?). And it makes live so much easier for me - I am running
> the simulations non-interactive on a cluster, and starting grass, which then
> starts R was always a hassle.
>
> What about adding a new option (errorOnExistingLocation=TRUE), which raises
> an error when the location exists?
>
> I assume that quite a few users are using R as a scripting language, and in
> this case, and consequently is more logical to me to have R as the base,
> which then initializes the grass environment when I need it, and not that I
> have to decide before I start R, if I have to start R in grass.
>
> I must admit, I am not to clear why it can be a problem when using
> initGRASS for an existing location (I know you explained it already, but I
> must have missed something).
>
> I remember reading that somebody was putting all the gras environmental
> variable initialization into .bash so that he/she can use grass from any
> terminal - so just setting the variables should be enough, if one is careful
> not to work in the same location from two different shells (i.e. grass
> sessions).
>

Found the link:
http://www.mail-archive.com/grass-user@lists.osgeo.org/msg06117.html


> So there are effectively two aspects of interfacing GRASS with R:
>
> 1) analysing spatial data which *is in R* with GRASS
> 2) analysing spatial data which *is in a GRASS database* with R
>
> I am using a mix of 1 and 2: my data comes from R and (mainly) a GRASS
> database, is processed in R and GRASS, and results are stored in the GRASS
> database.
>
> As the name of the location is determined in the parameter file (which is
> loaded into the R session), to go back to R inside grass would make things
> considerably more complex.
>
> By the way - how is python handling the link to GRASS? As I never used
> python, I have no idea how this works.
>
> Hope I will be able to convince you to leave the possibility in spgrass6,
>
> Cheers,
>
> Rainer
>
>  ...SNIP...
>
>> Roger
>>
>>
>>
>>> execGRASS("r.patch", flags=c("z"), parameters=list(input="**
>>> mangroves_1989_138_044_LR_**recl,mangroves_1989_138_045_**
>>> UL_recl,mangroves_1989_138_**045_UR_recl", output="testomat"), intern=T)
>>>
>>> Error in system(cmd0, intern = TRUE) :
>>>  Createprocess konnte 'C:\GRASS6~1.1\bin\RPATCH~1.**EXE
>>> --interface-description' nicht ausführen
>>> Fehler in parseGRASS(cmd) : r.patch not found
>>>
>>> I checked the GRASS directory and it is set right in the initGRASS
>>> command.
>>>
>>> I hope you can help me with one. I have no clue what to do!
>>>
>>> Thanks in advance,
>>>
>>> Tim
>>>
>>> ______________________________**_________________
>>> grass-stats mailing list
>>> grass-stats at lists.osgeo.org
>>> http://lists.osgeo.org/**mailman/listinfo/grass-stats<http://lists.osgeo.org/mailman/listinfo/grass-stats>
>>>
>>>
>> --
>> Roger Bivand
>> Department of Economics, NHH Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; fax +47 55 95 95 43
>> e-mail: Roger.Bivand at nhh.no
>> _______________________________________________
>> grass-stats mailing list
>> grass-stats at lists.osgeo.org
>> http://lists.osgeo.org/mailman/listinfo/grass-stats
>>
>>
>
>
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
> UCT), Dipl. Phys. (Germany)
>
> Centre of Excellence for Invasion Biology
> Stellenbosch University
> South Africa
>
> Tel :       +33 - (0)9 53 10 27 44
> Cell:       +33 - (0)6 85 62 59 98
> Fax (F):       +33 - (0)9 58 10 27 44
>
> Fax (D):    +49 - (0)3 21 21 25 22 44
>
> email:      Rainer at krugs.de
>
> Skype:      RMkrug
>
>


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax (F):       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer at krugs.de

Skype:      RMkrug
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