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

Tue Apr 19 06:41:25 PDT 2016

----------------------------------------
> Date: Mon, 18 Apr 2016 13:28:48 +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 Mon, 18 Apr 2016, Roger Bär wrote:
>
>> ----------------------------------------
>>> Date: Mon, 18 Apr 2016 10:40:02 +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 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)
>>
>> Yes, that would solve my issue indeed. Because I am using initGRASS
>> mostly in a permanent home with all my project data.
>
> Please download a development version from:
>
> http://win-builder.r-project.org/JZw14G61RjVk
>
> Set remove_GISRC=TRUE in the initGRASS() call, and use remove_GISRC() when
> you are through with this instance. I have included code to try to unlink
> the file and unset the environment variable when the R session terminates,
> but so far without success - you will need to remove it as described
> unless I see a way round a race condition.
>
> Roger (Bi)
>

Ok, thanks!
Roger (Bä)

>>
>> Roger (Bä)
>>
>>
>>>> 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
>
> --
> 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