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
}

Answer 1

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