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Python subprocess FileNotFoundError

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

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)

“git.exc.GitCommandNotFound: [WinError 2] The system cannot find the file specified” error in Python 3.5

I am trying to lemmatize a Latin text using Python 3.5 in Pycharm 5.0.4 with the CLTK library, but there seems to be a problem with Git. I get the error git.exc.GitCommandNotFound: [WinError 2] The system cannot find the file specified among other errors I believe are related—see below for the full output. I have tried adding a Git repository to the project folder and adding the git.exe path to version control but that seems to have done nothing. What can I do to get Git to work properly—please keep in mind that I am a complete neophyte when it comes to Python in particular and not very experienced with programming in general.
Code:
from cltk.stem.lemma import LemmaReplacer
from cltk.stem.latin.j_v import JVReplacer
from cltk.corpus.utils.importer import CorpusImporter
corpus_importer = CorpusImporter('latin')
corpus_importer.import_corpus('latin_text_latin_library')
corpus_importer.import_corpus('latin_models_cltk')
#corpus_importer.import_corpus('phi5', '~/PHI5/')
#t.convert_corpus(corpus='phi5')
j = JVReplacer()
lemmatizer = LemmaReplacer('latin')
In = open("CIC.txt","rt")
Out = open("CIC4.txt","wt")
text = In.read()
text = text.lower()
text = j.replace(text)
Out.write(str(lemmatizer.lemmatize(text)))
In.close()
Out.close()
Output:
C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\python.exe "C:\Program Files (x86)\JetBrains\PyCharm 5.0.4\helpers\pydev\pydevd.py" --multiproc --qt-support --client 127.0.0.1 --port 58508 --file C:/Users/Rune/PycharmProjects/untitled/Pucker.py
pydev debugger: process 14648 is connecting
Connected to pydev debugger (build 143.1919)
--- Logging error ---
Traceback (most recent call last):
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\site-packages\git\cmd.py", line 604, in execute
**subprocess_kwargs
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\subprocess.py", line 950, in __init__
restore_signals, start_new_session)
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\subprocess.py", line 1220, in _execute_child
startupinfo)
File "C:\Program Files (x86)\JetBrains\PyCharm 5.0.4\helpers\pydev\pydev_monkey.py", line 387, in new_CreateProcess
return getattr(_subprocess, original_name)(appName, patch_arg_str_win(commandLine), *args)
FileNotFoundError: [WinError 2] The system cannot find the file specified
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\site-packages\cltk\corpus\utils\importer.py", line 134, in import_corpus
Repo.clone_from(git_uri, target_dir, depth=1)
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\site-packages\git\repo\base.py", line 885, in clone_from
return cls._clone(git, url, to_path, GitCmdObjectDB, progress, **kwargs)
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\site-packages\git\repo\base.py", line 826, in _clone
v=True, **add_progress(kwargs, git, progress))
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\site-packages\git\cmd.py", line 450, in <lambda>
return lambda *args, **kwargs: self._call_process(name, *args, **kwargs)
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\site-packages\git\cmd.py", line 878, in _call_process
return self.execute(make_call(), **_kwargs)
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\site-packages\git\cmd.py", line 607, in execute
raise GitCommandNotFound(str(err))
git.exc.GitCommandNotFound: [WinError 2] The system cannot find the file specified
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\logging\__init__.py", line 980, in emit
msg = self.format(record)
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\logging\__init__.py", line 830, in format
return fmt.format(record)
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\logging\__init__.py", line 567, in format
record.message = record.getMessage()
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\logging\__init__.py", line 330, in getMessage
msg = msg % self.args
TypeError: not enough arguments for format string
Call stack:
File "C:\Program Files (x86)\JetBrains\PyCharm 5.0.4\helpers\pydev\pydevd.py", line 2411, in <module>
globals = debugger.run(setup['file'], None, None, is_module)
File "C:\Program Files (x86)\JetBrains\PyCharm 5.0.4\helpers\pydev\pydevd.py", line 1802, in run
launch(file, globals, locals) # execute the script
File "C:\Program Files (x86)\JetBrains\PyCharm 5.0.4\helpers\pydev\_pydev_imps\_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "C:/Users/Rune/PycharmProjects/untitled/Pucker.py", line 5, in <module>
corpus_importer.import_corpus('latin_text_latin_library')
File "C:\Users\Rune\AppData\Local\Programs\Python\Python35-32\lib\site-packages\cltk\corpus\utils\importer.py", line 136, in import_corpus
logger.error("Git clone of '%s' failed: '%s'", (git_uri, e))
Message: "Git clone of '%s' failed: '%s'"
Arguments: (('https://github.com/cltk/latin_text_latin_library.git', GitCommandNotFound('[WinError 2] The system cannot find the file specified',)),)
Process finished with exit code 0

You can manually download the corpus from https://github.com/cltk/latin_models_cltk and place it in the
~/cltk_data/latin/model/ folder (so ~/cltk_data/latin/model/latin_models_cltk/lemmata/ is an existing folder afterwards). Then you should be able to run the following just fine:
from cltk.stem.lemma import LemmaReplacer
LemmaReplacer('latin').lemmatize('some_latin_here')
For the same in Greek, just replace the 'latin' by 'greek' everywhere in these instructions. I imagine (but haven't tried) that it works the same for other languages too.

I am pretty sure that CLTK does not work with any Python version below 3.6, at least as of August 2017. I had a devil of a time getting 3.6 installed on Ubuntu (Ubuntu linus running dual boot from my PC laptop) but eventually got it to work. Also I specifically solved the problem that OP articulates above by following the instructions at https://disiectamembra.wordpress.com/2016/07/01/current-state-of-the-cltk-latin-lemmatizer/. Good luck!

Calling Popen in Python on a MAC - Error can not find file

When I try to shell out of my Python 3.51 program to run the Popen command I get the following errors. Yet when I copy the exact string I'm passing to Popen to the Terminal command line it works fine and opens the file in Adobe Reader which is my default app for the .pdf files.
Here is the Code:
finalCall = r'open /Users/gbarnabic/Documents/1111/combined.pdf'
print(finalCall)
pid_id = subprocess.Popen(finalCall).pid
Here is the error:
open /Users/gbarnabic/Documents/1111/combined.pdf
Exception in Tkinter callback
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/tkinter/init.py", line 1549, in call
return self.func(*args)
File "pdfcomb2.py", line 212, in change_dir
self.openPDF(outFileName, pageNum)
File "pdfcomb2.py", line 426, in openPDF
subprocess.run(finalCall)
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/subprocess.py", line 696, in run
with Popen(*popenargs, **kwargs) as process:
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/subprocess.py", line 950, in init
restore_signals, start_new_session)
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/subprocess.py", line 1544, in _execute_child
raise child_exception_type(errno_num, err_msg)
FileNotFoundError: [Errno 2] No such file or directory: 'open /Users/gb/Documents/1111/combined.pdf'
Georges-MBP:filepicktest gb$ open /Users/gb/Documents/1111/combined.pdf
Georges-MBP:filepicktest gb$

With Popen you need to set shell=True to pass command as a string or split command in a list of arguments. Could be done with shlex
import shlex
import subprocess
subprocess.Popen(shlex.split('open ....'))
You could check example in documentation:
https://docs.python.org/2/library/subprocess.html#subprocess.Popen
So the error here means that Python try to run file with name open /Users/gb/Documents/1111/combined.pdf. Obviously it doesn't exist

File txt: FileNotFoundError: [Errno 2] No such file or directory

i have a txt file and if i try to open it python says:
runfile('/Users/costanzanaldi/Desktop/tesi/Tesi_Naldi/COdice _Python/untitled0.py', wdir='/Users/costanzanaldi/Desktop/tesi/Tesi_Naldi/COdice _Python')
Traceback (most recent call last):
File "<ipython-input-30-b4bdfdd17ca2>", line 1, in <module>
runfile('/Users/costanzanaldi/Desktop/tesi/Tesi_Naldi/COdice _Python/untitled0.py', wdir='/Users/costanzanaldi/Desktop/tesi/Tesi_Naldi/COdice _Python')
File "/Users/costanzanaldi/anaconda/lib/python3.4/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 685, in runfile
execfile(filename, namespace)
File "/Users/costanzanaldi/anaconda/lib/python3.4/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 85, in execfile
exec(compile(open(filename, 'rb').read(), filename, 'exec'), namespace)
File "/Users/costanzanaldi/Desktop/tesi/Tesi_Naldi/COdice _Python/untitled0.py", line 13, in <module>
in_file = open("POLO_SCIENTIFICO_(LAMMA).txt","r")
FileNotFoundError: [Errno 2] No such file or directory: 'POLO_SCIENTIFICO_(LAMMA).txt'
1)the file EXISTS!
2)the path is correct! It is in the desktop!

You need to change your directory to your desktop in order to access the file. You'd do that using the os module, like this:
import os
os.chdir("/path/to/Desktop")

Presumably this means the file is not on the desktop. (I assume you changed Ethan's "/path/to/Desktop" to the correct path in your system, which is "/Users/costanzanaldi/Desktop"?). Wherever it is, you need to give open() the full path to POLO_SCIENTIFICO_(LAMMA).txt unless you have chdir'd to the correct directory. I assume you have got the letter-case correct in POLO_SCIENTIFICO_(LAMMA).txt :-)

Compiling and Executing Java file in python

how can I open an java file in python?, i've search over the net and found this:
import os.path, subprocess
from subprocess import STDOUT, PIPE
def compile_java (java_file):
subprocess.check_call(['javac', java_file])
def execute_java (java_file):
cmd=['java', java_file]
proc=subprocess.Popen(cmd, stdout = PIPE, stderr = STDOUT)
input = subprocess.Popen(cmd, stdin = PIPE)
print(proc.stdout.read())
compile_java("CsMain.java")
execute_java("CsMain")
but then I got this error:
Traceback (most recent call last):
File "C:\Python33\lib\subprocess.py", line 1106, in _execute_child
startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\casestudy\opener.py", line 13, in <module>
compile_java("CsMain.java")
File "C:\casestudy\opener.py", line 5, in compile_java
subprocess.check_call(['javac', java_file])
File "C:\Python33\lib\subprocess.py", line 539, in check_call
retcode = call(*popenargs, **kwargs)
File "C:\Python33\lib\subprocess.py", line 520, in call
with Popen(*popenargs, **kwargs) as p:
File "C:\Python33\lib\subprocess.py", line 820, in __init__
restore_signals, start_new_session)
File "C:\Python33\lib\subprocess.py", line 1112, in _execute_child
raise WindowsError(*e.args)
FileNotFoundError: [WinError 2] The system cannot find the file specified
>>>
the python file and java file is in the same folder, and I am using Python 3.3.2, how can I resolve this? or do you guys have another way on doing this?, any answer is appreciated thanks!

I think it isn't recognizing the javac command. Try manually running the command and if javac isn't a recognized command, register it in your PATH variable and try again.
Or you could just try typing the full pathname to the Java directory for javac and java.

you need to add path to your java file name. like this:
compile_java("C:\\path\to\this\CsMain.java")