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I'm trying to run R from the command line using command line arguments. This includes passing in some filepaths as arguments for use inside the script. It all works most of the time, but sometimes the paths have spaces in and R doesn't understand.

I'm running something of the form:

R CMD BATCH --slave "--args inputfile='C:/Work/FolderWith SpaceInName/myinputfile.csv' outputfile='C:/Work/myoutputfile.csv'" RScript.r ROut.txt

And R throws out a file saying

Fatal error: cannot open file 'C:\Work\FolderWith': No such file or directory

So evidently my single quotes aren't enough to tell R to take everything inside the quotes as the argument value. I'm thinking this means I should find a way to delimit my --args using a comma, but I can't find a way to do this. I'm sure it's simple but I've not found anything in the documentation.

The current script is very basic:

ca = commandArgs(trailingOnly=TRUE)
eval(parse(text=ca))
tempdata = read.csv(inputFile)
tempdata$total = apply(tempdata[,4:18], 1, sum)
write.csv(tempdata, outputFile, row.names = FALSE)

In case it's relevant I'm using windows for this, but it seems like it's not a cmd prompt problem.

mnel
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user1878693
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3 Answers3

3

Using eval(parse()) is probably not the best and most efficient way to parse command line arguments. I recommend to use a package like the optparse to do the parsing for you. Parsing command line args has already been solved, no need to reimplement this. I could imagine that this solves your problems. Although, spaces in path names are a bad idea to begin with.

Alternatively, you could take a very simple approach and pass the arguments like this:

R CMD BATCH --slave arg1 arg2

Where you can retrieve them like:

ca = commandArgs(TRUE)
arg1 = ca[2]
arg2 = ca[3]

This avoids the eval(parse which I think is causing the issues. Finally, you could try and escape the space like this:

R CMD BATCH --slave "C:/spam\ bla"

You could also give Rscript a try, R CMD BATCH seems to be less favored than Rscript.

Paul Hiemstra
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  • Using visual studio and the default test directory it makes has a space in it. I blame Microsoft :( I'll try this and be back with a reply shortly – user1878693 Dec 05 '12 at 11:18
  • But I would definitely try the optparse package. Or you could try an even simpler means of passing cmd line args, see my post. – Paul Hiemstra Dec 05 '12 at 11:20
  • Your third option doesn't work as apparently R doesn't understand "\ " as an escape character for space (within the --args at least). Second option looks like it shouldn't work because the arguments are still space delimited so it will thing there are 4 arguments when there are 3, if you see what I mean? – user1878693 Dec 05 '12 at 11:39
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    If you have arguments with spaces, then you need to enclose them within quotes, for example: `Rscript my_script.R arg1 'hello world' arg3` will run `my_script.R` with three arguments. This is more of a unix thing than R if you want to research it. – flodel Dec 05 '12 at 12:20
  • @flodel the OP already used quotes in his original question. Is this problem caused by using `R CMD BATCH` or by using `eval(parse())`... – Paul Hiemstra Dec 05 '12 at 15:04
1

As an enhancement of @PaulHimestra answer here how you can use Rscript :

you create a launcher.bat ,

echo off
C:
PATH R_PATH;%path%
cd DEMO_PATH
Rscript youscript.R arg1 arg2
exit

with R_PATH something like C:/Program Files/R/R-version

agstudy
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  • and even better, you can put the path to `Rscript` at the top of your `yourscript.R` (this is called a *shebang*), make your script executable, maybe even remove the `.R` extension and move the script to a directory in your `PATH`. Then you can just call `yourscript arg1 arg2` from anywhere. – flodel Dec 05 '12 at 12:25
  • Or on linux to be even more fancy `#! /usr/bin/env Rscript`. – Paul Hiemstra Dec 05 '12 at 15:04
1

There are many similarities with this post: R command line passing a filename to script in arguments (Windows)

Also this post is very OS related. My answer applies only to Windows.

Probably what you are looking for is RScript.exe instead of R.exe. The latter has no problem with spaces: path\to\RScript "My script.r".

One boring thing may be searching or setting the path for RScript and doing this every time one updates R.

Among the convenience scripts I have in my search path, I wrote a little facility to run RScript without bothering with paths. Just in case it may be of interest for someone:

@echo off
setlocal 


::Get change to file dir par (-CD must be 1st par)
::================================================
Set CHANGEDIR="F"
If /I %1 EQU -cd  (
 Set CHANGEDIR="T"
 SHIFT        
)       

::No args given
::=============
If [%1] EQU [] GoTo :USAGE 

::Get R path from registry 
::========================
:: may check http://code.google.com/p/batchfiles for updates on R reg keys
Call :CHECKSET hklm\software\R-core\R  InstallPath
Call :CHECKSET hklm\software\wow6432Node\r-core\r InstallPath
if not defined RINSTALLPATH echo "Error: R not found" & goto:EOF

::Detect filepath when arg not starting with "-" 
::==============================================

::Note the space after ARGS down here!!!
Set ARGS= 
:LOOP          
if [%1]==[] (GoTo :ELOOP)
Set ARGS=%ARGS% %1
::Echo [%ARGS%] 

Set THIS=%~1
if [%THIS:~0,1%] NEQ [-] (Set FPATH=%~dp1)

SHIFT          
GoTo :LOOP
:ELOOP        
::echo  %FPATH%


::Run Rscript script, changing to its path if asked
::=================================================
If %CHANGEDIR%=="T" (CD %FPATH%)
Echo "%RINSTALLPATH%\bin\Rscript.exe" %ARGS%
"%RINSTALLPATH%\bin\Rscript.exe" %ARGS%



endlocal 
:: ==== Subroutines ====
GoTo :EOF  

:USAGE       
Echo USAGE:
Echo  R [-cd] [RScriptOptions] Script [ScriptArgs]

Echo.          
Echo  -cd changes to script dir. Must be first par. 
Echo  To get RScript help on options etc.:
Echo  R --help

GoTo :EOF  


:CHECKSET  
if not defined RINSTALLPATH for /f "tokens=2*" %%a in ('reg query %1 /v %2 2^>NUL') do set RINSTALLPATH=%%~b
GoTo :EOF

The script prints the actual RScript invoking line, before running it.

Note that there is an added argument, -cd, to change automatically to the script directory. In fact it is not easy to guess the script path from inside R (and set it with setwd()), in order to call other scripts or read/write data files placed in the same path (or in a relative one).

This (-cd) might possibly make superfluous your other commandargs, as you may find convenient calling them straight from inside the script.

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antonio
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