I am trying to use
var <- as.numeric(readline(prompt="Enter a number: "))
and later use this in a calculation.
It works fine when running in RStudio but I need to be able to pass this input from the command line in Windows 10
I am using a batch file with a single line
Rscript.exe "C:\My Files\R_scripts\my_script.R"
When it gets to the user input part it freezes and it doesn't provide expected output.
From the documentation of readline():
This can only be used in an interactive session. [...] In non-interactive use the result is as if the response was RETURN and the value is "".
For non-interactive use - when calling R from the command line - I think you've got two options:
Use readLines(con = "stdin", n = 1) to read user input from the terminal.
Use commandArgs(trailingOnly = TRUE) to supply the input as an argument from the command line when calling the script instead.
Under is more information.
1. Using readLines()
readLines() looks very similar to readline() which you're using, but is meant to read files line by line. If we instead of a file points it to the standard input (con = "stdin") it will read user input from the terminal. We set n = 1 so that it stops reading from the command line when you press Enter (that is, it only read one line).
Example
Use readLines() in a R-script:
# some-r-file.R
# This is our prompt, since readLines doesn't provide one
cat("Please write something: ")
args <- readLines(con = "stdin", n = 1)
writeLines(args[[1]], "output.txt")
Call the script:
Rscript.exe "some-r-file.R"
It will now ask you for your input. Here is a screen capture from PowerShell, where I supplied "Any text!".
Then the output.txt will contain:
Any text!
2. UsingcommandArgs()
When calling an Rscript.exe from the terminal, you can add extra arguments. With commandArgs() you can capture these arguments and use them in your code.
Example:
Use commandArgs() in a R-script:
# some-r-file.R
args <- commandArgs(trailingOnly = TRUE)
writeLines(args[[1]], "output.txt")
Call the script:
Rscript.exe "some-r-file.R" "Any text!"
Then the output.txt will contain:
Any text!
Related
I am trying to use
var <- as.numeric(readline(prompt="Enter a number: "))
and later use this in a calculation.
It works fine when running in RStudio but I need to be able to pass this input from the command line in Windows 10
I am using a batch file with a single line
Rscript.exe "C:\My Files\R_scripts\my_script.R"
When it gets to the user input part it freezes and it doesn't provide expected output.
From the documentation of readline():
This can only be used in an interactive session. [...] In non-interactive use the result is as if the response was RETURN and the value is "".
For non-interactive use - when calling R from the command line - I think you've got two options:
Use readLines(con = "stdin", n = 1) to read user input from the terminal.
Use commandArgs(trailingOnly = TRUE) to supply the input as an argument from the command line when calling the script instead.
Under is more information.
1. Using readLines()
readLines() looks very similar to readline() which you're using, but is meant to read files line by line. If we instead of a file points it to the standard input (con = "stdin") it will read user input from the terminal. We set n = 1 so that it stops reading from the command line when you press Enter (that is, it only read one line).
Example
Use readLines() in a R-script:
# some-r-file.R
# This is our prompt, since readLines doesn't provide one
cat("Please write something: ")
args <- readLines(con = "stdin", n = 1)
writeLines(args[[1]], "output.txt")
Call the script:
Rscript.exe "some-r-file.R"
It will now ask you for your input. Here is a screen capture from PowerShell, where I supplied "Any text!".
Then the output.txt will contain:
Any text!
2. UsingcommandArgs()
When calling an Rscript.exe from the terminal, you can add extra arguments. With commandArgs() you can capture these arguments and use them in your code.
Example:
Use commandArgs() in a R-script:
# some-r-file.R
args <- commandArgs(trailingOnly = TRUE)
writeLines(args[[1]], "output.txt")
Call the script:
Rscript.exe "some-r-file.R" "Any text!"
Then the output.txt will contain:
Any text!
I am new to command line usage and don't think this question has been asked elsewhere. I'm trying to adapt an Rscript to be run from the command line in a shell script. Basically, I'm using some tools in the immcantation framework to read and annotate some antibody NGS data, and then to group sequences into their clonal families. To set the similarity threshold, the creators recommend using a function in their shazam package to set an appropriate threshold.
I've made the simple script below to read and validate the arguments:
#!/usr/bin/env Rscript
params <- commandArgs(trailingOnly=TRUE)
### read and validate mode argument
mode <- params[1]
modeAllowed <- c("ham","aa","hh_s1f","hh_s5f")
if(!(mode %in% modeAllowed)){
stop(paste("illegal mode argument supplied. acceptable values are",
paste(paste(modeAllowed, collapse = ", "), ".", sep = ""), "\nmode should be supplied first",
sep = " "))
}
### execute function
cat(threshold)
The script works, however since for each parameter there's only a finite number of options. I was wondering if there was a way of passing in the arguments like --mode aa (for example) from the terminal? All the information I've seen online seems to be using code like my mode <- params[1] from above which I guess only works if the mode argument is first?
currently, in this code below, there is manual intervention I want to define the path of 2 input files. but then I am not sure how to do it
library("openxlsx")
nm=readline("Enter data file name:")
readline("Enter input file name: (Press Enter)")
input_file=read.xlsx(file.choose())
I want to add paths to line 3,4 to arguments so far I have tried this but it isn't correct
library("openxlsx")
args = commandArgs(trailingOnly=TRUE)
nm=C:\Program Files\R-3.5.2\bin\tdd_data.xlsx
input_file=C:\Program Files\R-3.5.2\bin\tdd_rinput.xlsx
when I execute the code it gives me an error
***Error in source("tddarg.r") : tddarg.r:5:6: unexpected '/'
4: args = commandArgs(trailingOnly=TRUE)
5: nm=C:/***
you can make some changes and get exactly what you want.
nm="C:/Program Files/R/R-3.5.2/bin/tdd_data1.xlsx"
input_file=read.xlsx("C:/Program Files/R/R-3.5.2/bin/tdd_rinput2.xlsx")
I've only changed the slashes and added the read function to it.
I need help with passing an argument as a variable name in an R script from the terminal. I'll run the script as follows:
R < script.R --args "hello"
And, in the script there should be something like this:
args <- commandArgs(trailingOnly = TRUE)
assign(args[1],24)
save(args[1], file="output.RData")
But, I need to take the argument as the variable name. What I mean is the following: If I run the script with "numbers" argument, the variable name inside the script should be numbers.
assign(args[1], 24)
does the trick. But, inside the save function, args[1] does not work. How can I pass it as a variable name?
Does it work if you try
saveRDS(get(args[1]),file="output.rds")
?
You won't get a text file with the save function. If you want its text version you would need to use `dump". This would "work" despirte the extention. The file ois still an .Rdata file event without the extension:
arg=1
argname="reports"
assign(argname, arg)
reports
#[1] 1
save(reports, file="test.txt")
rm(reports)
rm(argname)
rm(arg)
load("test.txt")
To use dump:
dump('reports', file="test2.txt")
This would appear in that file. It should be parse-able (and readable to humans) R code:
reports <-
1
Have a fully working R-script. When executing it from Rscript it doesn't stop to accept user input however.
The user input is some readline statements. The cat statements prompting for input works as intended. Have I missed something?
I execute 'Rscript scriptfile.R' from terminal on macOS.
You can create a function typeline() to read an input line and then use the result for your next commands. It will wait for your input text either you run your code in Rstudio or in terminal:
typeline <- function(msg="Enter text: ") {
if (interactive() ) {
txt <- readline(msg)
} else {
cat(msg);
txt <- readLines("stdin",n=1);
}
return(txt)
}
txt=typeline("your message: ")
print(txt)
Managed to get it to work by changing readline to readLines as mentioned in the post suggested by meenaparam. The downside with this method is that ithe script only works in batch mode, running it in Rstudio makes it hang. Would be good to know a general way to capture keyboard input i.e that works both in interactive and batch mode.
Use this
cat("What's your name? ")
name <- readLines(file("stdin"),1)
cat("What's your age? ")
age <- readLines(file("stdin"),1)
print(name)
print(age)