Changing directories in Rscript

Question

How can I have my Rscript parameters change directories?

If my command-line argument is Rscript test.R "foo1", I want to setwd("~/foo1"), but I get the error that it cannot change working directory.

args<-commandArgs(trailingOnly=TRUE) 
lambda<args[1] 
fileEnd<-args[2] 
replicate<-args[3] 
directory<-args[4] 
setwd(directory)

A sample command-line is Rscript test.R 0 1 10 "~/foo1"

Have you checked if the directory you are trying to change to exists. Can you post your code? — asb, Jun 18 '14 at 20:56
In addition , is is not a good practice to change directory within the script. — agstudy, Jun 18 '14 at 21:06
But you don't mention why you want to change the directory? to source an R script ? or to read a text file? In both case better to use complete path and check if the file exists. — agstudy, Jun 18 '14 at 21:15
@MichaelHoffman "Error in setwd(file.path(path.expand('~'),directory)): cannot change current working directory" — user3746406, Jun 18 '14 at 21:23
@agstudy: Each directory has files I use to simulate, but the data is organized as results of their parameters, as titled by the directory. For each directory, I'm going to produce output files of the simulation's results. — user3746406, Jun 18 '14 at 21:24
Using setwd() in a script is perfectly fine as long as it is explicitly stated at the top of the script that any shared user should use their own appropriate directory. — Seanosapien, Apr 29 '18 at 10:10

rrs · Answer 1 · 2014-06-18T21:04:34.477

0

Try this:

# use commandline arguments
args <- commandArgs(TRUE)

# the first argument is the working dir
working.dir <- args[1]

# change the working dir
setwd(file.path("~", working.dir))

edited Jun 18 '14 at 21:04

answered Jun 18 '14 at 20:54

rrs

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Toolbox · Answer 2 · 2018-11-13T09:35:29.653

It is not possible to give you a specific answer since you are not providing the key parts of your script. To simplify the troubleshooting, start with adding the full physical path to what you want to change directory. This to secure that the full path works.

General suggestions.

The most structured way is to put an [.Rprofile] file in the directory you will trigger your Rscript. The local [.Rprofile] will be read when Rscript initiates the R terminal session. In [.Rprofile] you need to add [setwd('/yourpath'). This is assumed if you just want to set the wd at start.

If you need to change the [setwd] during the course of your script/s you can of course include them in the R-files. Remember though that Rstudio and R terminal behaves different when comes to [load/save]. Rstudio acts dynamically when you change something through its console and show directly the changes in the global environment window.

For Rscript triggered from terminal you will have to make sure that for each script you add [load/save] for R to compensate that it losses the environment when it is not in a running session with Rscript.

The difference behaviour between Rstudio and R terminal is important to keep in mind, especially if you test scenarios in Rstudio and expect it to work the same way in R-terminal.

Changing directories in Rscript

2 Answers2