[GRASS-stats] [R-sig-Geo] GISRC environment variable using initGRASS

Mon Apr 18 01:40:02 PDT 2016

On Mon, 18 Apr 2016, Roger Bär wrote:

>
>
> ----------------------------------------
>> Date: Sun, 17 Apr 2016 20:11:06 +0200
>> From: Roger.Bivand at nhh.no
>> To: baerroger at outlook.com
>> CC: grass-stats at lists.osgeo.org
>> Subject: RE: [R-sig-Geo] GISRC environment variable using initGRASS
>>
>> On Sat, 16 Apr 2016, Roger Bär wrote:
>>
>>> Thanks for the support!Please see below my comments.
>>>
>>>> Date: Fri, 15 Apr 2016 20:58:15 +0200
>>>> From: Roger.Bivand at nhh.no
>>>> To: baerroger at outlook.com
>>>> CC: r-sig-geo at r-project.org
>>>> Subject: Re: [R-sig-Geo] GISRC environment variable using initGRASS
>>>>
>>>> On Fri, 15 Apr 2016, Roger Bär wrote:
>>>>
>>>>> I am currently using the R package "rgrass7" (Version: 0.1-6) in order
>>>>> to command GRASS GIS (Windows7, OSGEO4W installation).
>>>>>
>>>>> I use R in order to start a GRASS environment and to script my
>>>>> geoprocessing. Both is working fine. However, I have problems with
>>>>> storing and calling the GRASS gisenv variables. Every time when I call
>>>>> "initGRASS" a file called "junk" is created containing GRASS gisenv
>>>>> variables.
>>>>>
>>>>
>>>> What the file is called is probably immaterial.
>>>>
>>>>>
>>>>> Looking at the source of the initGRASS function the section below
>>>>> puzzeled me somehow:
>>>>>
>>>>> 59 Sys.setenv(GISRC = paste(Sys.getenv("HOME"), "\\.grassrc7",
>>>>> 60 sep = ""))
>>>>
>>>> This is setting GISRC to a value
>>>
>>> Yes. The absolute path to the file (containing settings for GISDBASE,
>>> LOCATION_NAME and MAPSET)
>>>
>>>>> 61 if (file.exists(Sys.getenv("GISRC")) && !override)
>>>>> 62 stop("A GISRC file already exists; to override, set override=TRUE")
>>>>> 63 Sys.setenv(GISRC = "junk")
>>>>
>>>> This is setting it again in the working directory - I don't recall why -
>>>> probably frustration years ago with Windows.
>>>
>>> I really do not understand the "junk" (line 63). Because GISRC is set to
>>> "junk" the subsequent lines of code will write the GISRC environment
>>> variables to a newly created file called "junk" in the home folder.
>>> Shouldn't this line not rather be omitted? (The GRASS environment
>>> variables would then be written to ".grassrc7", which in my opinion
>>> would be correct)
>>
>> The name of the file is immaterial, but from an R script should only be
>> accessed from the value of the environment variable.
>>
>
> Ok.
>
>>>
>>>>
>>>>> 64 cat("GISDBASE:", getwd(), "\n", file = Sys.getenv("GISRC"))
>>>>> 65 cat("LOCATION_NAME: <UNKNOWN>", "\n", file = Sys.getenv("GISRC"),
>>>>> 66 append = TRUE)
>>>>> 67 cat("MAPSET: <UNKNOWN>", "\n", file = Sys.getenv("GISRC"),
>>>>> 68 append = TRUE)
>>>>> 69 gisrc <- ifelse(use_g.dirseps.exe, system(paste("g.dirseps.exe -g",
>>>>> 70 shQuote(Sys.getenv("GISRC"))), intern = TRUE), Sys.getenv("GISRC"))
>>>>> 71 assign("addEXE", .addexe(), envir = .GRASS_CACHE)
>>>>> 72 Sys.setenv(GISRC = gisrc)
>>>>>
>>>>
>>>> And this sets it again. It is set, otherwise GRASS wouldn't work;
>>>> programmatically you'd have to use Sys.getenv("GISRC") to get the value.
>>>> Please provide a use case where this matters, and consider moving this
>>>> thread to the statsgrass list.
>>>
>>> Sorry, I do not understand what you mean with "provide a use case where
>>> this matters". What do you mean with "this"?
>>
>> The use of an arbitrary name in a throw-away location is of no
>> significance, and could in the future be a short random name. My guess is
>> that the use of "junk" may have come from different file permissions on
>> unix and windows systems - if override is TRUE, R might end up trying to
>> write to a file that some other process is still blocking.
>>
>
> Ok. 
>
>> Unless you can provide an R script that I can run in WinNat (not OSGeo4W -
>> I do not have the time or patience to install multiple Windows versions of
>> GRASS that I never use), and which demonstrates that something more is
>> involved than the name of a temporary file, I can't help, because I do not
>> see any real problem - the name if the file is arbitrary, and in the R
>> session is accesses by Sys.getenv().
>
> Ok, I get that. The main issue was to keept the directory clean since 
> access my grass data from different operating system. But thinks it's 
> not worth to spend more time on this issue. (I'll survive the junk file 
> in my workspace)

Would it help to try to add an argument to initGRASS() to try to delete 
the file pointed at by GISRC on exit from the R session?

In many cases, the file is in R's temporary directory (home=tempdir()), so 
gets removed automatically, but if you are using a non-temporary home=, 
the file stays there.

Roger (Bi)

>
> Thanks you anyway!
>
>
> Regards,
> Roger  (Bä)
>
>
>
>
>>> I added the thread to the grass-stat list (and will remove r-sig from
>>> the cc the next time).
>>
>> OK,
>>
>> Roger (Bi)
>>
>>> Roger
>>>
>>>>
>>>> Hope this helps (doesn't clarify, but that's legacy Windows),
>>>>
>>>> Roger
>>>>
>>>>> First, why is initGRASS using ".grassrc7" for storing the GISRC file?
>>>>> InitGRASS is looking for the GISRC file under ".grassrc7" (line 59). However, in the package documentation [1], the GISRC file is called ".gisrc". Moreover, the GRASS documentation says that the GISRC file is stored under "/.grass7/rc"
>>>>>
>>>>> Second, what is the purpose of assigning "junk" to the GISRC environment variable?
>>>>> GISRC is set to "junk" (line 63) and then the GISRC value ("junk") is assigned again back to system variable GISRC. Unless I misinterpreded the code, it does not make much sense to me. Shouldn't the enviroment varibales not be written (line 64 - 68) to ".grassrc7" rather than to "junk"?
>>>>>
>>>>>
>>>>>
>>>>> I would appreciate any support or hints!
>>>>>
>>>>> Regards,
>>>>> Roger
>>>>>
>>>>> [1] http://https//cran.r-project.org/web/packages/rgrass7/rgrass7.pdf
>>>>> [2] http://grass.osgeo.org/grass70/manuals/variables.html
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-Geo mailing list
>>>>> R-sig-Geo at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>
>>>> --
>>>> Roger Bivand
>>>> Department of Economics, Norwegian School of Economics,
>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>> voice: +47 55 95 93 55; fax +47 55 95 91 00
>>>> e-mail: Roger.Bivand at nhh.no
>>>> http://orcid.org/0000-0003-2392-6140
>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>> http://depsy.org/person/434412
>>>
>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; fax +47 55 95 91 00
>> e-mail: Roger.Bivand at nhh.no
>> http://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>> http://depsy.org/person/434412

-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
http://depsy.org/person/434412