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GRASS with R interface issues - running R within GRASS 6.4.2
4 messages · Laura S, Roger Bivand
On Mon, 23 Apr 2012, Laura S wrote:
Dear all: Should I reinstall GRASS and set up some sort of path, so that R is recognized? Would anyone be able to send me key words to find more basic, newbie, information on "PATH" and "R_LIBS"? I would like to find the paths, and set the proper variables, but I am unsure where to start. I have fiddled in GRASS now without R, but I would like to use R within GRASS.?
Please do try to search more effectively. The standard way of running R inside GRASS on Windows is to start GRASS first in the location you are using, then enter the complete path to R at the MSYS prompt. The complete path is the same as the string shown as Target: under Properties if you right-click on the R icon on your Windows desktop. For example: "C:/Program Files/R/R-2.15.0/bin/i386/Rgui.exe" or the equivalent for your installation. You may also need to set the environment variable R_LIBS if R cannot "find" the correct library containing the packages you need. If you are not using a GRASS location, you may use the initGRASS() function in spgrass6 to start a temporary GRASS session, often in a throw-away location, because you only need to move objects from R to GRASS, use GRASS on them, and move the output objects back to R. Then you need the complete path to the GRASS install directory, for example: "C:/Program Files/GRASS 6.4.2" or the equivalent for your installation. It is also possible to use initGRASS() with existing locations in a scripting context, but this is not your case. The grass-stats mailing list is often used for questions like this. Hope this clarifies, Roger
Which location should I do all this in? There are more than option for GRASS, e.g., command line, GUI (with MSYS, without, etc.), MSYS UNIX console; I am not sure which one to use for loading R within GRASS. Any suggestions are much appreciated. Thank you, Laura
Dear all: I am trying to get
R to run with grass, but I am running into trouble.
This is what I have done so far: Installed GRASS 6.4.2 for Windows XP Installed spgrass6 with dependencies. When I do: library(spgrass6) gmeta6() I get the following: Error in system(cmd0,intern=TRUE); "g.region.exe' not found Error in parseGRASS(cmd) : g.region not found.
Any suggestions are much appreciated. I am new to using GRASS with R, but I am looking forward to using them together to analyze data.
I am unsure which terminal to run R in GRASS because I keep getting errors in the command console in GRASS: I type into either "Command console in GRASS GIS Layer Manager" OR "GRASS Command Line":
R ...Then I get 'R' is not recognized as an internal or external command, operable program or batch file.
This suggests that you need to give the complete path to R from within your GRASS session. It may be "C:/Program Files/R/R-2.14.1/bin/Rgui.exe" or something like that, depending on where you installed it. You may also need to add R_LIBS="<whatever>" to this, to show where any local libraries may be. Alternatively, you may try to add R's binary location to your PATH environment variable, and declare R_LIBS globally; these used to be under advanced system properties. Finally, as Rainer suggests, you may start GRASS from within R, using the same logic in reverse, giving the full path to the GRASS install location to the initGRASS() function. The key in both cases is to find out where in your file system the software components live, and note changes when you upgrade. Hope this helps, Roger [[alternative HTML version deleted]]
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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On Mon, 23 Apr 2012, Laura S wrote:
Dear Roger and others: My apologies if I am not piecing everything together. I think I am almost there; I appreciate your patience. This is my current point of confusion, and what I am able to do so far: I. My main point of confusion is that when I type the path into GRASS MSYS, the R console window pops up, and I am unable to type more into the GRASS console. I cannot type GRASS commands in R, so I am unsure where I type the GRASS commands if GRASS console does not let me type more, and the R console does not recognize R commands.
Why should it? Simply minimise the R GUI to work in GRASS directly, using the GRASS GUI or from the prompt in MSYS. I doubt very much whether saying d.ask makes sense anyway, as the GRASS display GUI covers that. It is possible to write GRASS commands using execGRASS() from the R console, but since you have had to ask, you will find it easier simply to minimise R and use GRASS directly. Because R is within GRASS, it "sees" the current status of the location. Hope this clarifies - please change to one of the GRASS lists for further help. Roger
II. What I can do so far in more detail:
1. Within the GRASS 6.4.2RC2 with
MSYS, I typed using tab autocompletion: "C:/Program
Files/R/R-2.14/bin/i386/Rgui.exe" which causes the RGui to pop up as a
second R window. Thus, I am not in GRASS directly anymore I assume, but
rather in the RGui. In this GUI, it says the following when I type
library(spgrass6):
"GRASS GIS Interface loaded with GRASS version GRASS 6.4.2RC2exported (2011) and location: demolocation"
gmeta6()
gisdbase C:/Documents etc.?
If I try a GRASS command such as "d.ask" in the RGUI after loading spgrass:
d.ask
Error: object 'd.ask' not found
2. I can also get this to work in R directly:
loc <- initGRASS("C:/Program Files/Grass 6.4",home=tempdir())
gmeta6()
**prints gisdbase, etc.**?
d.ask
Error: object 'd.ask' not found
Thank you for your help,
Laura
________________________________ From: Roger Bivand <Roger.Bivand at nhh.no> To: Laura S <les_ecol at yahoo.com> Cc: "r-sig-geo at r-project.org" <r-sig-geo at r-project.org> Sent: Monday, April 23, 2012 2:21:16 AM Subject: Re: [R-sig-Geo] GRASS with R interface issues - running R within GRASS 6.4.2 On Mon, 23 Apr 2012, Laura S wrote: Dear all: Should I reinstall GRASS and set up some sort of path, so that R is recognized? Would anyone be able to send me key words to find more basic, newbie, information on "PATH" and "R_LIBS"? I would like to find the paths, and set the proper variables, but I am unsure where to start. I have fiddled in GRASS now without R, but I would like to use R within GRASS.? Please do try to search more effectively. The standard way of running R inside GRASS on Windows is to start GRASS first in the location you are using, then enter the complete path to R at the MSYS prompt. The complete path is the same as the string shown as Target: under Properties if you right-click on the R icon on your Windows desktop. For example: "C:/Program Files/R/R-2.15.0/bin/i386/Rgui.exe" or the equivalent for your installation. You may also need to set the environment variable R_LIBS if R cannot "find" the correct library containing the packages you need. If you are not using a GRASS location, you may use the initGRASS() function in spgrass6 to start a temporary GRASS session, often in a throw-away location, because you only need to move objects from R to GRASS, use GRASS on them, and move the output objects back to R. Then you need the complete path to the GRASS install directory, for example: "C:/Program Files/GRASS 6.4.2" or the equivalent for your installation. It is also possible to use initGRASS() with existing locations in a scripting context, but this is not your case. The grass-stats mailing list is often used for questions like this. Hope this clarifies, Roger Which location should I do all this in? There are more than option for GRASS, e.g., command line, GUI (with MSYS, without, etc.), MSYS UNIX console; I am not sure which one to use for loading R within GRASS. Any suggestions are much appreciated. Thank you, Laura Dear all: I am trying to get R to run with grass, but I am running into trouble. This is what I have done so far: Installed GRASS 6.4.2 for Windows XP Installed spgrass6 with dependencies. When I do: library(spgrass6) gmeta6() I get the following: Error in system(cmd0,intern=TRUE); "g.region.exe' not found Error in parseGRASS(cmd) : g.region not found. Any suggestions are much appreciated. I am new to using GRASS with R, but I am looking forward to using them together to analyze data. I am unsure which terminal to run R in GRASS because I keep getting errors in the command console in GRASS: I type into either "Command console in GRASS GIS Layer Manager" OR "GRASS Command Line": R ...Then I get 'R' is not recognized as an internal or external command, operable program or batch file. This suggests that you need to give the complete path to R from within your GRASS session. It may be "C:/Program Files/R/R-2.14.1/bin/Rgui.exe" or something like that, depending on where you installed it. You may also need to add R_LIBS="<whatever>" to this, to show where any local libraries may be. Alternatively, you may try to add R's binary location to your PATH environment variable, and declare R_LIBS globally; these used to be under advanced system properties. Finally, as Rainer suggests, you may start GRASS from within R, using the same logic in reverse, giving the full path to the GRASS install location to the initGRASS() function. The key in both cases is to find out where in your file system the software components live, and note changes when you upgrade. Hope this helps, Roger ??? [[alternative HTML version deleted]] -- 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
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