Python subprocess FileNotFoundError

Question

I am trying to follow this blog on how to execute an R script from Python. I have the R script working fine from the command line using Rscript.

Here's my Python code:

import subprocess
import os

command = "C:\Program Files\R\R-3.4.4\bin\Rscript"
path2script = os.getcwd() + "\max.R" # gives me the absolute path to the R script
args = ["11", "3", "9", "42"]

cmd = [command, path2script] + args
x = subprocess.check_output(cmd, universal_newlines = True)

Which gives me this error:

FileNotFoundError: [WinError 2] The system cannot find the file specified

I've read a lot of SO posts on this error and in most cases it seems to be a problem with trying to invoke system commands like dir or passing arguments to check_output in the wrong order but in my case I really don't see what should be going wrong.

Following some of the advice I've tried building a string for cmd instead of a list, and then passing it to check_output using the argument shell = True - when I do that I get a CalledProcessError: returned non-zero exit status 1.

I'm assuming this code, which is exactly as it appeared on the blog other than adding the absolute path to the file, is failing now because the behaviour of check_output has changed since 2015...

Can anyone help?

Here's the stack trace:

Traceback (most recent call last):

  File "<ipython-input-2-3a0151808726>", line 1, in <module>
    runfile('C:/Users/TomWagstaff/Documents/Raising IT/Projects/15 AdWords/Python_R_test/run_max.py', wdir='C:/Users/TomWagstaff/Documents/Raising IT/Projects/15 AdWords/Python_R_test')

  File "C:\Users\TomWagstaff\Anaconda3\envs\adwords\lib\site-packages\spyder\utils\site\sitecustomize.py", line 705, in runfile
    execfile(filename, namespace)

  File "C:\Users\TomWagstaff\Anaconda3\envs\adwords\lib\site-packages\spyder\utils\site\sitecustomize.py", line 102, in execfile
    exec(compile(f.read(), filename, 'exec'), namespace)

  File "C:/Users/TomWagstaff/Documents/Raising IT/Projects/15 AdWords/Python_R_test/run_max.py", line 31, in <module>
    x = subprocess.check_output(cmd, universal_newlines = True)

  File "C:\Users\TomWagstaff\Anaconda3\envs\adwords\lib\subprocess.py", line 336, in check_output
    **kwargs).stdout

  File "C:\Users\TomWagstaff\Anaconda3\envs\adwords\lib\subprocess.py", line 403, in run
    with Popen(*popenargs, **kwargs) as process:

  File "C:\Users\TomWagstaff\Anaconda3\envs\adwords\lib\site-packages\spyder\utils\site\sitecustomize.py", line 210, in __init__
    super(SubprocessPopen, self).__init__(*args, **kwargs)

  File "C:\Users\TomWagstaff\Anaconda3\envs\adwords\lib\subprocess.py", line 709, in __init__
    restore_signals, start_new_session)

  File "C:\Users\TomWagstaff\Anaconda3\envs\adwords\lib\subprocess.py", line 997, in _execute_child
    startupinfo)

FileNotFoundError: [WinError 2] The system cannot find the file specified

Is this method called anywhere in your stack error trace? "NamedTemporaryFile()" — hshantanu, Dec 04 '18 at 19:23
You should try with a forward slash(`/`) - `path2script = os.getcwd() + "/max.R"` — Mortz, Dec 05 '18 at 10:34

score 2 · Accepted Answer · answered Dec 05 '18 at 10:56

check that you have a right path for command and script

print(os.path.exists(command))
print(os.path.exists(path2script))

note that writing path with backslashes may be dangerous as you can create escape sequence that way which will be interpreted in different way. You can write windows paths with forward slashes and then call os.path.normpath on them, turning them into safe form (also in command you can use forward slashes only, Python interpret doesn't really care. In path to your R script that would be probably problem though)

This was it! Just discovered that my "\bin" was becoming a special character (backspace?) in the final string. Escaping the backslash like so: "\\bin" throughout the `command` string fixed the issue... — Tom Wagstaff, Dec 05 '18 at 11:01

Python subprocess FileNotFoundError

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