[GRASS-stats] Re: spgrass6 and initGRASS
Patrick Giraudoux
patrick.giraudoux at univ-fcomte.fr
Tue Dec 8 02:17:43 EST 2009
Roger Bivand a écrit :
> On Mon, 7 Dec 2009, Roger Bivand wrote:
>
>> On Mon, 7 Dec 2009, Patrick Giraudoux wrote:
>>
>>> Dear Roger,
>>>
>>> I have moved the thread and the answer below from
>>> qgis-user at lists.osgeo.org to this list as advised...
>>>>
>>>> That is because the GRASS environment variables have not been set
>>>> at that point. Do you need to use GRASS in throw-away (initGRASS)
>>>> mode, or with an existing location? If the latter, please use the
>>>> interface in the regular way, starting R "within" GRASS. I'll try
>>>> to reproduce the problem, but it is not easy to do, I'm afraid.
>>
>> Dear Patrick,
>>
>> I've tried with Metis with no success. The first problem is addressed
>> in this draft release:
>>
>> http://spatial.nhh.no/R/Devel/spgrass6_0.6-13.zip
>>
>> but with Metis is simply falls over later. With WinGRASS (last but
>> latest), it just works. It even works in Metis once the basic GRASS
>> framework is set up using WinGRASS, but behaviour is erratic and
>> unpredictable. To track it with Metis (which I just uninstalled to
>> try OSGeo4W) seemed impossible, it wasn't clear where the GRASS
>> modules were looking for their environment variables and GISRC
>> backstore.
>>
>> I would probably use file transfer and have QGIS do the desktop
>> mapping and WinGRASS the analytical stuff, but I can't say that I
>> have favourites here.
>
>
> I've now installed QGIS 1.3.0 Mimas and GRASS 6.4.0 SVN from OSGeo4W.
> Doing it their way (rather than my way), you then need Carson Farmer's
> ManageR plugin and the rpy2 2.0.6 msi for python 2.5 (the one that
> OSGeo4W ships). Next probably you need to put your R (mine is 2.10.0)
> on the PATH which OSGeo4W and QGIS have manipulated - maybe through
> the control panel - needs updating manually.
>
> Start QGIS, look for Carson's repository, install and enable manageR,
> open a GRASS mapset in QGIS, enter library(spgrass6) in the manageR
> console, and if you're lucky GRASS may be there. I've managed to move
> spearfish roads to R and tabulate road length by class using
> SpatialLinesLength() on the representation on the R side. Fairly
> horrible to install for students, but maybe?
>
> Roger
>
Yes indeed. That was a concern to me. The previous standalone versions
of QGIS metis was good enough and R could simply be started from within
a GRASS session (console) in QGIS... and the OSGEO4W SVN Kore and Mimas
were the same. I am using R 2.10.0 too. Except that in all versions any
error in R led to quit and come back to the GRASS console... I have
already exported R objects (eg "gmeta6" files) that way. On the other
hand, GRASS commands were quite OK to manage with the console (but no
copy and paste function available...).
My hope with initGRASS was just to avoid opening a GRASS session and to
read files from R with gmeta6, and maybe readRAST6, readVECT6 without
having to start/working with GRASS or QGIS.... Looks like being out of
reach yet with QGIS/GRASS under Windows.
Anyway thanks for having had a look and for all the work done with
spgrass6 (and others !)
Best,
Patrick
>>
>>>
>>> I would like to be capable to read into GRASS locations from within
>>> R (so not from R started withing GRASS) -what is supposedly done
>>> with initGRASS; eg just to pick up a region definition into a
>>> "spgrass6" object and compute on that. I though that initGRASS was
>>> design for this task.
>>>
>>
>> Right, initGRASS with home=tempdir() (not what I replied earlier -
>> with no home= given, it uses whatever Windows says "HOME" is) starts
>> a new location and mapset in the R temporary directory, which you
>> move data to for GRASS to analyse.
>>
>>>> Have you tried the WinGRASS stand-alone (I haven't trusted either
>>>> QGIS GRASS used this way or OSGeo4W - I follow the bug-tracker for
>>>> OSGEO4W, so stay away)?
>>>
>>> I am trying this essentially on teaching purposes. Students are
>>> working under Windows XP and Vista. I have only a limited number of
>>> hours, and to board GIS concepts from QGIS then to GRASS is somehow
>>> easier for them than straight within GRASS (although it is just the
>>> reverse when you know GRASS). The QGIS Metis standalone version was
>>> excellent for that. You have seen that the updates to Kore and Mimas
>>> are done with no standalone version available on the QGIS official
>>> site. There the use of OSGeo4W is encouraged and I am trying to find
>>> out what could be best advisable for the students.
>>>
>>> I did not tried WinGRASS yet, and I am interested in doing it, but
>>> have installed the OSGeo4W GRASS 6.4svn version (works well - but
>>> definitely the unix/linux environment is more convenient for command
>>> lines), as well as OSGeo4W QGIS Kore and Mimas, and try and compare
>>> them.
>>>
>>
>> Roger
>>
>>>> What is your sessionInfo()?
>>> sessionInfo()
>>> R version 2.10.0 (2009-10-26)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3]
>>> LC_MONETARY=French_France.1252 LC_NUMERIC=C [5]
>>> LC_TIME=French_France.1252 attached base packages:
>>> [1] grDevices datasets splines graphics stats tcltk
>>> utils [8] methods base other attached packages:
>>> [1] spgrass6_0.6-12 XML_2.6-0 rgdal_0.6-22 sp_0.9-47
>>> [5] svSocket_0.9-48 TinnR_1.0.3 R2HTML_1.59-1 Hmisc_3.7-0
>>> [9] survival_2.35-7
>>>
>>> loaded via a namespace (and not attached):
>>> [1] cluster_1.12.1 grid_2.10.0 lattice_0.17-26 svMisc_0.9-56
>>> [5] tools_2.10.0 Roger Bivand a écrit :
>>>> On Mon, 7 Dec 2009, Patrick Giraudoux wrote:
>>>>
>>>>> Have tried the following:
>>>>>
>>>>> initGRASS("C:\\OSGeo4W\\bin",home="U:\\Documents and
>>>>> Settings\\pgiraudo\\",override=T)
>>>>> initGRASS("C:\\Program Files\\Quantum
>>>>> GIS\\grass",home="U:\\Documents and Settings\\pgiraudo",override=T)
>>>>> initGRASS("C:\\OSGeo4W\\bin",override=T)
>>>>>
>>>>> with the same results...
>>>>>
>>>>>> initGRASS("C:\\OSGeo4W\\bin",home="U:\\Documents and
>>>>> Settings\\pgiraudo\\",override=T)
>>>>> Error in system(paste("g.dirseps.exe -g",
>>>>> shQuote(Sys.getenv("WINGISRC"))), :
>>>>> g.dirseps.exe not found
>>>>>> initGRASS("C:\\Program Files\\Quantum
>>>>>> GIS\\grass",home="U:\\Documents and
>>>>> Settings\\pgiraudo",override=T)
>>>>> Error in Sys.setenv(GISRC = gisrc) : wrong length for argument
>>>>>> initGRASS("C:\\OSGeo4W\\bin",override=T)
>>>>> Error in Sys.setenv(GISRC = gisrc) : wrong length for argument
>>>>>
>>>>> Quite puzzling since g.dirseps does not give a message "unknown
>>>>> command" when tried within grass (thus it is suppose to be in the
>>>>> GRASS programme)
>>>>
>>>> That is because the GRASS environment variables have not been set
>>>> at that point. Do you need to use GRASS in throw-away (initGRASS)
>>>> mode, or with an existing location? If the latter, please use the
>>>> interface in the regular way, starting R "within" GRASS. I'll try
>>>> to reproduce the problem, but it is not easy to do, I'm afraid.
>>>>
>>>> What is your sessionInfo()? Have you tried the WinGRASS stand-alone
>>>> (I haven't trusted either QGIS GRASS used this way or OSGeo4W - I
>>>> follow the bug-tracker for OSGEO4W, so stay away)?
>>>>
>>>> Would you mind moving to the proper list - this is a GRASS question
>>>> much more than an R one:
>>>>
>>>> http://lists.osgeo.org/mailman/listinfo/grass-stats
>>>>
>>>> Roger
>>>>
>>>>>
>>>>> Patrick
>>>>>
>>>>>
>>>>>
>>>>> Roger Bivand a écrit :
>>>>>> On Mon, 7 Dec 2009, Patrick Giraudoux wrote:
>>>>>>
>>>>>>> Here is the result:
>>>>>>>
>>>>>>> library(spgrass6)
>>>>>>>
>>>>>>> debug(initGRASS)
>>>>>>>> initGRASS("C:/OSGeo4W/bin",home="U:/Documents and
>>>>>>> Settings/pgiraudo/",override=T)
>>>>>>>
>>>>>>> (...)
>>>>>>>
>>>>>>> Browse[2]>
>>>>>>> debug: gisrc <- system(paste("g.dirseps.exe -g",
>>>>>>> shQuote(Sys.getenv("WINGISRC"))),
>>>>>>> intern = TRUE)
>>>>>>> Browse[2]> Sys.getenv("WINGISRC")
>>>>>>> WINGISRC
>>>>>>> "U:/Documents and Settings/pgiraudo/\\.grassrc6"
>>>>>>> Browse[2]> shQuote(Sys.getenv("WINGISRC"))
>>>>>>> [1] "\"U:/Documents and Settings/pgiraudo/\\.grassrc6\""
>>>>>>> Browse[2]> gisrc
>>>>>>> Error: object 'gisrc' not found
>>>>>>
>>>>>> Could you try both not setting home= (you get a temporary folder
>>>>>> that is deleted when you exit R), or setting
>>>>>>
>>>>>> home="U:\\Documents and Settings\\pgiraudo"
>>>>>>
>>>>>> without the trailing forward slash?
>>>>>>
>>>>>> This a problem connected to protecting spaces on the one hand and
>>>>>> system specific directory separators on the other, I think.
>>>>>>
>>>>>> Roger
>>>>>>
>>>>>>>
>>>>>>> Beforehand, the first time I run
>>>>>>> initGRASS("C:/OSGeo4W/bin",home="U:/Documents and
>>>>>>> Settings/pgiraudo/",override=T), I got:
>>>>>>>
>>>>>>> initGRASS("C:/OSGeo4W/bin",home="U:/Documents and
>>>>>>> Settings/pgiraudo/",override=T)
>>>>>>> Error in system(paste("g.dirseps.exe -g",
>>>>>>> shQuote(Sys.getenv("WINGISRC"))), :
>>>>>>> g.dirseps.exe not found
>>>>>>>
>>>>>>> Then, if I try the same commande on QGIS Metis, I got:
>>>>>>> initGRASS("C:/Program Files/Quantum
>>>>>>> GIS/grass",home="U:/Documents and Settings/pgiraudo",override=T)
>>>>>>> Error in Sys.setenv(GISRC = gisrc) : wrong length for argument
>>>>>>>
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Patrick
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Roger Bivand a écrit :
>>>>>>>> On Sun, 6 Dec 2009, Patrick Giraudoux wrote:
>>>>>>>>
>>>>>>>>> Dear all,
>>>>>>>>>
>>>>>>>>> I am trying to init a GRASS session from within R, using the
>>>>>>>>> function initGRASS from the package spgrass6. GRASS is
>>>>>>>>> installed in two ways on my computer (here, the OS is Windows
>>>>>>>>> XP): with QGIS metis (precompiled version including grass 6.3
>>>>>>>>> (2008)) and grass 6.4.0svn, just freshly installed with the
>>>>>>>>> Osgeo4W installer.
>>>>>>>>>
>>>>>>>>> In both cases I get the same result:
>>>>>>>>>
>>>>>>>>>> initGRASS("C:/Program Files/Quantum
>>>>>>>>>> GIS/grass",home="U:/Documents and
>>>>>>>>> Settings/pgiraudo",override=T)
>>>>>>>>> Error in Sys.setenv(GISRC = gisrc) : wrong length for argument
>>>>>>>>>
>>>>>>>>>> initGRASS("C:/OSGeo4W/bin",home="U:/Documents and
>>>>>>>>> Settings/pgiraudo",override=T)
>>>>>>>>> Error in Sys.setenv(GISRC = gisrc) : wrong length for argument
>>>>>>>>>
>>>>>>>>> Any idea about what happens ?
>>>>>>>>
>>>>>>>> No, without the output of traceback(), it isn't obvious,
>>>>>>>> although here traceback() might not help. Run under
>>>>>>>> debug(initGRASS) to the step before, that is:
>>>>>>>>
>>>>>>>> gisrc <- system(paste("g.dirseps.exe -g",
>>>>>>>> shQuote(Sys.getenv("WINGISRC"))), intern=TRUE)
>>>>>>>>
>>>>>>>> then run:
>>>>>>>>
>>>>>>>> Sys.getenv("WINGISRC")
>>>>>>>> shQuote(Sys.getenv("WINGISRC"))
>>>>>>>> gisrc
>>>>>>>>
>>>>>>>> and try to see what is going on. At this stage,
>>>>>>>> Sys.getenv("GISRC") should be "junk", assigned a couple of
>>>>>>>> lines earlier.
>>>>>>>>
>>>>>>>> Maybe the grass-stats list would have a higher proportion of
>>>>>>>> users of both GRASS and R.
>>>>>>>>
>>>>>>>> Hope this helps,
>>>>>>>>
>>>>>>>> Roger
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Patrick
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>>
>
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