graphviz.backend.ExecutableNotFound: failed to execute ['dot', '-Tpng'], make sure the Graphviz executables are on your systems' PATH

Question

I wasn't able to find any solution to this issue for one hour and decided better to ask here. The only rich info is given here with no detailed instructions to match my case.

I am on Windows 10, using PyCharm to connect to offline Ubuntu 16.04 server to try some machine learning classification.

The code is working to some point, then throwing this

Traceback (most recent call last):
  File "/home/user/.local/lib/python3.5/site-packages/graphviz/backend.py", line 159, in run
    proc = subprocess.Popen(cmd, startupinfo=get_startupinfo(), **kwargs)
  File "/usr/lib/python3.5/subprocess.py", line 947, in __init__
    restore_signals, start_new_session)
  File "/usr/lib/python3.5/subprocess.py", line 1551, in _execute_child
    raise child_exception_type(errno_num, err_msg)
FileNotFoundError: [Errno 2] No such file or directory: 'dot'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/user/project/2_input/xgboost_loop.py", line 55, in <module>
    xgb.plot_tree(classifier, ax=plt.gca())
  File "/home/user/.local/lib/python3.5/site-packages/xgboost/plotting.py", line 281, in plot_tree
    s.write(g.pipe(format='png'))
  File "/home/user/.local/lib/python3.5/site-packages/graphviz/files.py", line 138, in pipe
    quiet=quiet)
  File "/home/user/.local/lib/python3.5/site-packages/graphviz/backend.py", line 229, in pipe
    out, _ = run(cmd, input=data, capture_output=True, check=True, quiet=quiet)
  File "/home/user/.local/lib/python3.5/site-packages/graphviz/backend.py", line 162, in run
    raise ExecutableNotFound(cmd)
graphviz.backend.ExecutableNotFound: failed to execute ['dot', '-Tpng'], make sure the Graphviz executables are on your systems' PATH

Process finished with exit code 1

I checked via pip list that I do have graphviz version 0.13.2 on Ubuntu server. One suggested in the above given link that the output of whereis dot should be added as os.environ["PATH"] += os.pathsep + 'OUTPUT' to the file to be run, but there isn't any output except dot:.

Locally, I also checked that I have the same graphviz version 0.13.2.

Sapro

Answer 1

try sudo apt-get install graphviz

Vibrate

Answer 2

You have to add the graphviz binaries to your system PATH variable. On my system that's C:\Program Files\Graphviz 2.44.1\bin\

Lombardy