Call R Script from Python with arguments

Question

I have a r Script with the code:

args = commandArgs(trailingOnly=TRUE)
myData <- read.csv(file=args[0])

I want to run this using a GUI and deliver a choosen csv file with this python code

from tkinter import filedialog
from tkinter import *
import subprocess

window = Tk()
window.geometry('500x200')
window.title("Wordcloud Creator")
lbl = Label(window, text="1. Please prepare a CSV (-Trennzeichen) file with the columns untgscod, berpos, SpezX3")
lbl.grid(column=0, row=0)
def runScript():
    filename = filedialog.askopenfilename(initialdir = "/",title = "Select file",filetypes = (("csv files","*.csv"),("all files","*.*")))
    subprocess.call(['Rscript', 'C:/Users/Name/Desktop/R-GUI/test.r', filename])
btn = Button(window, text="Select a file and start Cloud creation", command=runScript())
btn.grid(column=0, row=1)
window.mainloop()

But unfortunately this is not working. I get this error but do not know what is wrong.

  File "c:\Users\name\.vscode\extensions\ms-python.python-2019.2.5558\pythonFiles\lib\python\ptvsd\_vendored\pydevd\_pydev_bundle\pydev_monkey.py", line 444, in new_CreateProcess
    return getattr(_subprocess, original_name)(app_name, patch_arg_str_win(cmd_line), *args)
FileNotFoundError: [WinError 2] The system cannot find the file specified

I do not see why the file cannot be found.

Is your path correct? The FileNotFoundError informs me that you might have given it a relative path but that is not the path in which the file resides — Mike Tung
– Mike Tung, Commented Mar 27, 2019 at 13:18
Possible duplicate of Using a Windows path within Python's subprocess (point to an executable) [beginner] — Bram Vanroy
– Bram Vanroy, Commented Mar 27, 2019 at 13:26
I added filename = '"' + filename + '"' and filename.replace("\\", "/") but still get the same error. print(filename) gives me "C:/Users/name/Desktop/file.csv" — ruedi
– ruedi, Commented Mar 27, 2019 at 13:45
Is Python script running in same environment as R? Also, use os.path.join() from built-in os module for os-agonstic file paths. Check if Python can see path with os.path.exists(). Finally, do note, R has its own GUI modules: gWidgets2, RGtk2, rattle! — Parfait
– Parfait, Commented Mar 27, 2019 at 13:50
The environment variable was not set correct. FileNotFoundError is a bit confusing here. Thanks for your help! — ruedi
– ruedi, Commented Mar 27, 2019 at 16:39

Oka · Accepted Answer · 2019-03-27 14:03:08Z

0

As suggested in comments, check that

your paths are correct and do not contain empty spaces or weird characters
files do exist in correct location

...and if it doesn´t help, you could try to use subprocess.run instead of subprocess.call.

edited Mar 27, 2019 at 14:03

answered Mar 27, 2019 at 13:56

Oka

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Comments

Nick · Accepted Answer · 2019-03-27 15:26:56Z

0

I don't know anything about python, so I can't help you there, but your Rscript is calling the zeroth element of your arguments, which is just an empty character.

R starts indexing at 1.

so if my script was:

args <- commandArgs(trailingOnly = TRUE)
print(args[0])

it would return:

[1] character(0) # this is R telling you that the atomic is a character, but it has zero length

Your RScript should be:

args <- commandArgs(trailingOnly = TRUE)
MyData <- read.csv(file = args[1])

Also, if that's your whole Rscript, 'MyData' is going to disappear as soon as that RScript closes. If you want to create a file in R, you'll need to use:

write.table(<whatever>)

with the appropriate arguments for your data.

answered Mar 27, 2019 at 15:26

Nick

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1 Comment

ruedi Over a year ago

Thany you. I would have been run into this without your help.

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