[R-sig-Geo] spgrass6: execGRASS: make the output of the command an R object.

[Rainer M. Krug]

Roger Bivand <Roger.Bivand at nhh.no> writes:

> On Mon, 20 May 2013, Paulo van Breugel wrote:
>
>> Great, this is really helpful. You are right, and I should have seen from
>> the help file, that the semicolon is not one of the supported separators.
>> The odd thing is it works when running r.univar from grass directly if I
>> use the table flag (-t instead of -g). But now I know I shouldn't.
>
> With GRASS 7:
>
> a <- execGRASS("r.univar", flags = "t", map = "elevation.dem",
>  separator="; ", intern = TRUE)
>
> works, but:
>
> a <- execGRASS("r.univar", flags = "t", map = "elevation.dem",
>   separator=";", intern = TRUE)
>
> does not. The problem is that the trailing ";" on the command line to
> GRASS is also the shell line terminator, so must be protected by
> quoting:
>
> a <- execGRASS("r.univar", flags = "t", map = "elevation.dem",
>   separator="';'", intern = TRUE)
>
> or:
>
> a <- execGRASS("r.univar", flags = "t", map = "elevation.dem",
> separator=shQuote(";"), intern = TRUE)

Following the escaping: I can not think about any problems, if all
arguments for grass are quoted (OK - I am speaking from the Linux side
without enough Windows experience with R to know if it works there as
well). Escaping *all* arguments *automatically* should make
execGRASS even more stable?

Rainer

>
> both work.
>
> Roger
>
>
>>
>> Thanks for helping out, much appreciated!
>>
>> Paulo
>>
>>
>>
>>
>>
>> On Mon, May 20, 2013 at 7:38 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
>>
>>> On Mon, 20 May 2013, Paulo van Breugel wrote:
>>>
>>>  Hi
>>>>
>>>> In older version of the execGRASS function of spgrass6, setting the option
>>>> intern=TRUE would make the output of the grass command a R object.
>>>>
>>>> Now, when I run execGRASS with the intern=TRUE, like the statement below,
>>>> the output is not written to the R object.
>>>>
>>>> a <- execGRASS("r.univar", flags="g", map=distmod, separator=";",
>>>> intern=TRUE)
>>>>
>>>
>>> With GRASS 6.4.2:
>>>
>>> a <- execGRASS("r.univar", flags = "g", map = "elevation.dem", intern =
>>> TRUE)
>>>
>>> works as before. Adding the fs= parameter causes the failure. You are
>>> using GRASS 7, in which fs= is separator=. In:
>>>
>>> raster/r.univar/r.univar_main.**c
>>>
>>> only \\t, tab, space, and comma are defined as such, others seem to be
>>> accepted, but ";" is not. I think that the parameter is unused anyway in
>>> script-style output, but setting fs=";" certainly causes trouble.
>>>
>>> Try without that parameter. Your observed difference in behaviour is not
>>> intended from the R side, and is caused by odd behaviour and interaction
>>> between parameters on the GRASS side in this GRASS module for your
>>> parameter settings. Other GRASS modules, and r.univar with different fs=
>>> settings, work as expected on Unix platforms, but under Windows, legacy
>>> execution is enforced anyway.
>>>
>>> Hope this clarifies,
>>>
>>> Roger
>>>
>>>
>>>> The object 'a' is created, but it is empty (character(0)). However, when I
>>>> set legacyExec=TRUE (like below), the object 'a' is created with the grass
>>>> r.univar output.
>>>>
>>>> a <- execGRASS("r.univar", flags="g", map=distmod, separator=";",
>>>> legacyExec=TRUE, intern=TRUE)
>>>>
>>>> Is this the intended behaviour (i.e., did I miss something in the help
>>>> file)?
>>>>
>>>> I am running R version 3.0.1 (2013-05-16), on Ubuntu 13.04 64-bit
>>>>
>>>> Paulo
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
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>>>>
>>>>
>>> --
>>> 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
>>>
>>>
>>
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-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

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