Wait for user input when running an R script in Linux

Question

I am have a piece of code that prompts for user input and works perfectly fine in while running the code in Windows. However, in Linux, it executes every line without waiting for user input.

I have added the code in a separate function and used system("stty -echo") without success. Why is this happening and what can be done ? (execution command : Rscript test.R)

require(Biostrings)
read_value <- function(prompt_text = "", prompt_suffix = getOption("prompt"),
                       coerce_to= "character")
{
  prompt <- paste(prompt_text, prompt_suffix)
  system("stty -echo")
  as(readline(prompt), coerce_to)
 }

prints<-function()
{ opt<-as.character(readline(prompt = "Enter parameter values: "))
  system("stty -echo")
  i<-1
  while ((i<=5))
    { if (i==1)
       { expr.filename <- as.character(readline(prompt = "Expression file name: "))
         tryCatch( {expr.file<-read.table(expr.filename)},error=function(e)
             {print("ERROR : Enter valid filename!") return })
       }
      if (i==2)
      {  system("stty -echo")
       fasta.filename <- as.character(readline(prompt = "Fasta file name: "))
       tryCatch( {sequence_data<-read.DNAStringSet(fasta.filename)},error=function(e) 
                {print("ERROR : Enter valid filename!")  return })
      }
     #missing piece of code
    i<-i+1
}

How are you running `Rscript test.R` in Windows? Are you running it from the Windows command line? I ask because `readline` shouldn't prompt for user input when called from a non-interactive session, regardless of the platform. — Joshua Ulrich, Mar 10 '12 at 19:05
@Joshua Ulrich - I am running it in Linux using that command. — agatha, Mar 10 '12 at 19:11
@JoshuaUlrich- However, I would like to have an interactive session, on Linux — agatha, Mar 10 '12 at 19:16

IRTFM · Accepted Answer · 2012-03-10T19:14:20.307

7

You might want to consider using readLines from "stdin". The prompt function is designed for documenting datasets.

 cat("Please enter a file name ...")
 fil <- readLines(con="stdin", 1)
 cat(fil, "\n")

Save as filnam.r .... Use:

user-linux-prompt$  Rscript filnam.r

edited Mar 10 '12 at 19:14

answered Mar 10 '12 at 19:06

IRTFM

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-I have tried it and it works as it is..I was trying to adapt it to my code to see how it works.. – agatha Mar 10 '12 at 19:28

Wait for user input when running an R script in Linux

1 Answers1