R script from command line

Question

I wanted to run this example script: http://mazamascience.com/WorkingWithData/?p=912 from Windows command line. So I opened the command line and typed Rscript tryCatch.R 1. However, I keep getting the error message Error: R not found. I did set the PATH environment variable as C:\Programme\R\R-3.0.1\bin. If I just type R.exe, it does start R, but it cannot find the packages that are to be loaded at start (e.g. package 'utils' in options<"defaultPackages"> was not found). I guess I have to set another path to the libraries somewhere, but I haven't got any idea where to do this.

UPDATE: After explicitly typing PATH C:\Programme\R\R-3.0.1\bin (rather than just adding this to the value of the environment variable PATH) it seems that R is found. However, a new problem occurs: In normalizePath<path.expand(path), winslash, mustWork>: path[2] = "C:/Programme/R/R-3.0.1/library": Access denied, the same than for the methods library. Then: Calls: .First ... library -> .getRequiredPackages2 -> library -> normalizePath Execution stopped. I'm using Windows 7 and I do have administrator rights.

Try using R CMD BATCH tryCatch.R 1. You may have to alter the script to accept the command line arguments (if so I will post an full answer but I am curious to know if this works first) — Simon O'Hanlon
– Simon O'Hanlon, Commented Jun 27, 2013 at 10:15
@SimonO101 Thanks for your suggestion, but unfortunately I get the same error message (Error: R not found). — AnjaM
– AnjaM, Commented Jun 27, 2013 at 11:07
You might want to look at batchfiles.googlecode.com . Look at R.bat. e.g. R.bat script myscript.R, which is automatic but requires a reasonably standard installation or the RPathSet.bat alternative which is a flexible batch file in which you edit the variables and then run it prior to running R to set up your environment variables. There is a pdf that comes with it that documents it. — G. Grothendieck
– G. Grothendieck, Commented Jun 27, 2013 at 11:40
@G.Grothendieck Thanks for your suggestion, I'll have a look at this! — AnjaM
– AnjaM, Commented Jun 27, 2013 at 12:06

agstudy · Accepted Answer · 2013-06-27 11:29:20Z

8

Rscript is very handy (R CMD BATCH is the old way to ) specially under windows, But generally under I create a batch file to avoid all path's headache.

For example say launcher.bat:

@echo off
C:
PATH C:\Programme\R\R-3.0.1\bin;%path%
cd PATH_TO_YOUR_RSCRIPT
Rscript tryCatch.R 1
pause

And open a console(using cmd) , go where you have stored your launcher.bat and launch it. Or from the R cosnole using shell:

shell('path_to_launcher\launcher.bat')

answered Jun 27, 2013 at 11:29

agstudy

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4 Comments

AnjaM Over a year ago

Thanks for your suggestion, that's a good idea. Based on the content of your launcher-file, I've tried to explicitly define the PATH, which brought me one step forward, but still doesn't work properly. Once I'll get this fixed, I will try to run batch files.

agstudy Over a year ago

@AnjaM I don'understand why do you mean by explicitly defining PATH? What do you have as error.

AnjaM Over a year ago

I've updated my original question and described the new error there. By explicitly defining PATH I mean really writing PATH C:\Programme\R\R-3.0.1\bin in the command line before typing Rscript tryCatch.R 1 (the way you do it in your launcher-file). Previously, I just added the path to the PATH environment variable in Windows and thought this would be enough.

agstudy Over a year ago

Try first toi execute the script from R using source . Once you get it works, the method should work.

AnjaM · Accepted Answer · 2013-07-01 13:52:40Z

2

I've found out that it was a language-specific problem on Windows 7, similar to what is described here: https://stat.ethz.ch/pipermail/r-help/2011-May/276932.html

After changing PATH to C:\Program Files\R\R-3.0.1\bin the script is properly executed from the command prompt.

Thanks to everyone who tried to help!

answered Jul 1, 2013 at 13:52

AnjaM

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1 Comment

Julian Wise Over a year ago

thank you! To note we point the PATH variable at the \bin folder rather than directly targeting the .exe file

not_an_expert · Accepted Answer · 2014-12-29 15:07:12Z

0

I ran into this problem under windows 7, apparently, when setting environment variables>user variables the path is not added into the PATH, so the user must add this path in system variables > PATH at the end just add the path to your .EXE files and voila.

answered Dec 29, 2014 at 15:07

not_an_expert

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