"RuntimeError: Make sure the Graphviz executables are on your system's path" after installing Graphviz 2.38

Question

I downloaded Graphviz 2.38 MSI version and installed under folder C:\Python34, then I run pip install Graphviz, everything went well. In system's path I added C:\Python34\bin. When I tried to run a test script, in line filename=dot.render(filename='test'), I got a message

 RuntimeError: failed to execute ['dot', '-Tpdf', '-O', 'test'], make sure the Graphviz executables are on your systems' path

I tried to put "C:\Python34\bin\dot.exe" in system's path, but it didn't work, and I even created a new environment variable "GRAPHVIZ_DOT" with value "C:\Python34\bin\dot.exe", still not working. I tried to uninstall Graphviz and pip uninstall graphviz, then reinstall it and pip install again, but nothing works.

The whole traceback message is:

Traceback (most recent call last):
  File "C:\Python34\lib\site-packages\graphviz\files.py", line 220, in render
    proc = subprocess.Popen(cmd, startupinfo=STARTUPINFO)
  File "C:\Python34\lib\subprocess.py", line 859, in __init__
    restore_signals, start_new_session)
  File "C:\Python34\lib\subprocess.py", line 1112, 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:\Users\Documents\Kissmetrics\curves and lines\eventNodes.py", line 56, in <module>
    filename=dot.render(filename='test')
  File "C:\Python34\lib\site-packages\graphviz\files.py", line 225, in render
    'are on your systems\' path' % cmd)
RuntimeError: failed to execute ['dot', '-Tpdf', '-O', 'test'], make sure the Graphviz executables are on your systems' path

Does anybody have any experience with it?

score 214 · Answer 1 · edited Mar 08 '18 at 15:23

214

You should install the graphviz package in your system (not just the python package). On Ubuntu you should try:

sudo apt-get install graphviz

edited Mar 08 '18 at 15:23

Sainath Adapa

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answered Mar 18 '17 at 14:13

kame

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If this doesn't work (it says the package is referenced but not there or something like that) run `sudo apt-get update` in order to update apt-get and tell it what packages are there. – Pro Q Jan 21 '18 at 00:39
If you're in a Docker Container (like I was), I was already at `root` and only needed `apt-get install graphviz` – kevin_theinfinityfund Jun 15 '20 at 17:00
Hope I can help someone with this. It did not work the first time for me so I ran `sudo apt-get update && sudo apt-get upgrade` and it worked afterwards. – dylanvanw Apr 15 '21 at 11:15
What if I just want to install graphviz in a virtual environment? – Vadim May 26 '23 at 17:59

score 184 · Answer 2 · edited Aug 21 '23 at 11:58

184

This one should solve the problem on MacOS:

brew install graphviz

To explain the misconception for new comer who using Conda. When we run conda install graphviz, it install the binary of Graphviz (this is not executable in Phyton yet).

And then we usually will also install conda install python-graphviz, this install the wrapper for phyton to run the binary of graphviz, the problem is we might get errors with message "graphviz" not exececuteable.

Thus why better use homebrew to install Graphviz binary and then install python-graphviz. Homebrew will guarantee the binary executeable.

edited Aug 21 '23 at 11:58

GusDeCooL

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answered Jul 30 '16 at 02:46

Rouzbeh

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For mac, it seem this is best option. Unless you want to use MacPorts and install graphviz from here: http://www.graphviz.org/Download_macos.php. – Alex Nov 25 '16 at 19:14
How do I find my bin folder where I have graphviz. I am having this problem and is really killing right now. Just checked I have graphviz 2.38. – Herc01 Feb 21 '19 at 16:05
Before brew install graphviz worked I had to run: xcode-select --install – Va5ili5 Feb 02 '22 at 13:59
Thank you. I installed graphviz with pip but only worked when I installed it with homebrew. – Leonardo Apr 10 '22 at 12:56
No brew does not. – sajid Aug 18 '22 at 08:17
This is what did it for my (mac os) – Renata Ghisloti Aug 07 '23 at 20:32

score 157 · Answer 3 · answered Jun 19 '17 at 08:43

157

import os
os.environ["PATH"] += os.pathsep + 'D:/Program Files (x86)/Graphviz2.38/bin/'

In windows just add these 2 lines in the beginning, where 'D:/Program Files (x86)/Graphviz2.38/bin/' is replaced by the address of where your bin file is.

That solves the problem.

answered Jun 19 '17 at 08:43

Aprameyo Roy

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worked in windows, I downloaded graphviz-2.38.zip from here https://graphviz.gitlab.io/_pages/Download/Download_windows.html. Unzip it and place it the mentioned folder – user3046442 Mar 14 '18 at 08:15
This works for me. I tried to add this to user and system environment variables, but that doesn't work, only your solution works for me. – Tom Oct 25 '18 at 17:05
this worked for me as well, but it threw another error before working. For some reason It gave me a side-by-side configuration....-error. I had to additionally reinstall the Microsoft Visual C++ 2008 Redistributable Package (x86). If someone has the same problem, here's the link: [https://www.microsoft.com/de-DE/download/details.aspx?id=29] – Marco Dec 29 '18 at 08:00
I used chocolatey to install graphviz `choco install -y graphviz` – reddi.tech Mar 20 '20 at 09:06
Yep this worked. make sure to download the right graphviz. I also placed the graphviz bins on both user and system paths. – max Oct 07 '20 at 22:03

score 94 · Answer 4 · edited Jul 09 '18 at 20:14

94

For Windows:

Install windows package from: https://graphviz.gitlab.io/_pages/Download/Download_windows.html
Install python graphviz package
Add C:\Program Files (x86)\Graphviz2.38\bin to User path
Add C:\Program Files (x86)\Graphviz2.38\bin\dot.exe to System Path

This worked for me!

edited Jul 09 '18 at 20:14

Pablo

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answered May 16 '17 at 15:05

Jyotsna_b

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Also Close your "cmd" in which jupyter notebook is running. Existing running CMD dont catch the new changes in Environment variables. – Rohit Nandi Apr 15 '18 at 08:46
4

It didn't work for me until I **restarted** the system – Mohammad Nazari Dec 04 '19 at 00:31
This worked perfectly. Just had to restart the notebook again. Thanks. – Amresh Giri Apr 20 '20 at 07:55
You don't need to restart the entire system, but just the python kernel. – SujaiSparks Jul 21 '22 at 10:04
@SujaiSparks - didn't work - I had to restart the entire system. – Alaa M. Jan 29 '23 at 19:27

Abishek · Answer 5 · 2018-11-03T23:51:46.337

64

Try using:

conda install python-graphviz

The graphviz executable sit on a different path from your conda directory, if you use pip install graphviz.

edited Nov 03 '18 at 23:51

answered Oct 29 '18 at 09:00

Abishek

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```Conda install graphviz``` worked on windows! nothing else seems to work :\ – Joel Carneiro Jan 29 '19 at 15:00
1

pygraphviz have a [nice big warning](https://pygraphviz.github.io/documentation/stable/install.html) against using conda, Not clear why, though. – Adam Burke Feb 24 '21 at 06:07
1

I ran `conda install python-graphviz` in my Anaconda prompt and once the execution is done, just restart the Jupyter notebook kernel. It worked for me. – mpriya Mar 03 '21 at 07:52
I ran conda install python-graphviz in my Anaconda prompt and once the execution is done, just restart the Jupyter notebook kernel. It worked for me. Worked on Windows as well. – Mata May 19 '23 at 14:01

score 26 · Answer 6 · answered May 19 '19 at 02:58

Step 1: Install Graphviz binary

Windows:

Download Graphviz from http://www.graphviz.org/download/
Add below to PATH environment variable (mention the installed graphviz version):
- C:\Program Files (x86)\Graphviz2.38\bin
- C:\Program Files (x86)\Graphviz2.38\bin\dot.exe
Close any opened Juypter notebook and the command prompt
Restart Jupyter / cmd prompt and test

Linux:

sudo apt-get update
sudo apt-get install graphviz
or build it manually from http://www.graphviz.org/download/

Step 2: Install graphviz module for python

pip:

pip install graphviz

conda:

conda install graphviz

Excellent explanation! Thank you~ – Bright Chang Jan 29 '20 at 07:33 — Bright Chang, Jan 29 '20 at 07:33

score 18 · Answer 7 · edited Mar 03 '20 at 12:28

18

This is showing some path issue:

pip install graphviz

So this worked for me:

sudo apt-get install graphviz

edited Mar 03 '20 at 12:28

mischva11

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answered Mar 03 '20 at 12:23

VARAT BOHARA

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sudo apt-get install graphviz is not alternative of pip install – sajid Aug 18 '22 at 08:20

score 16 · Answer 8 · answered Apr 26 '17 at 02:25

16

OSX Sierra, Python 2.7, Graphviz 2.38

Using pip install graphviz and conda install graphviz BOTH resolves the problem.

pip only gets path problem same as yours and conda only gets import error.

answered Apr 26 '17 at 02:25

Leighton

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ONLY this worked for me. after trying everything. thanks. – Meghna Natraj Jan 10 '19 at 19:35
```Conda install graphviz``` worked on windows! nothing else seems to work :\ – Joel Carneiro Jan 29 '19 at 14:59

score 16 · Answer 9 · answered May 23 '19 at 08:23

16

Using conda install graphviz and conda install python-graphviz to install GraphViz on Windows10 the path needed was C:/ProgramData/Anaconda3/Library/bin/graphviz/ for me. I.e. adding

import os
os.environ["PATH"] += os.pathsep + 'C:/ProgramData/Anaconda3/Library/bin/graphviz/'

solved the issue for me.

answered May 23 '19 at 08:23

rosa b.

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This def solved the issue... thanks – Zombraz Nov 05 '21 at 22:05

JessieB · Answer 10 · 2016-02-21T13:21:05.400

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Just add below to your Environmental Variable(system) PATH on Windows

C:\Program Files (x86)\Graphviz2.38\bin

there, you can find .exe files

If not work

Find Graphviz2.38/bin folder in your Program Files not in python lib

Then, add to your PATH

It's important to find a folder where .exe files exist

edited Feb 21 '16 at 13:21

answered Feb 19 '16 at 08:39

JessieB

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it seems only your post can solve my problem...win10 enterprise edition, jupyter notebook, py 3.6 – Travis May 21 '19 at 11:07
You will have to restart the jupyter notebook/annaconda for the environmental variables (PATH) to be re-cached. – SujaiSparks Jul 21 '22 at 10:07

score 10 · Answer 11 · answered Sep 16 '17 at 21:58

10

Try conda install graphviz. I had the same problem, I resolved it by mentioned command in MacOS.

answered Sep 16 '17 at 21:58

ajayramesh

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```Conda install graphviz``` worked on windows! nothing else seems to work :\ – Joel Carneiro Jan 29 '19 at 14:59

score 9 · Answer 12 · answered Nov 06 '19 at 19:11

9

On Ubuntu Linux this solved it for me:

pip install graphviz
sudo apt-get install graphviz

You could also try conda install -c conda-forge graphviz instead of pip if using Anaconda.

answered Nov 06 '19 at 19:11

wordsforthewise

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This worked for me in WSL in Windows 10 as well. Installation using pip was not enough. – Nerxis Feb 28 '20 at 08:06

score 8 · Answer 13 · edited Oct 06 '18 at 04:40

8

conda install python-graphviz

For Windows, install the Python Graphviz which will include the executables in the path.

edited Oct 06 '18 at 04:40

Unheilig

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answered Oct 06 '18 at 04:07

abhishek

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```Conda install graphviz``` worked on windows! nothing else seems to work :\ – Joel Carneiro Jan 29 '19 at 15:00

score 8 · Answer 14 · edited Mar 05 '20 at 14:44

8

When solving this issue for myself, I used this GitHub tutorial, which analysed the cause of this issue. If we read in between the lines, it says it needs system as well as python graph viz. In addition to conda install, we would need to run:

conda install -c conda-forge python-graphviz

Then restart the kernel; it works like a charm.

edited Mar 05 '20 at 14:44

Das_Geek

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answered Mar 05 '20 at 13:51

Jaya

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score 8 · Answer 15 · answered Mar 10 '20 at 10:08

I'm on macOS Catalina 10.15.3, and I had a similar error: ExecutableNotFound: failed to execute ['dot', '-Tsvg'], make sure the Graphviz executables are on your systems' PATH

Fixed it with:

pip3 install graphviz AND brew install graphviz

Note the pip3 install will only return the success message Successfully installed graphviz-0.13.2 so we still need to run brew install to get graphviz 2.42.3 (as of 10 Mar 2020, 6PM).

score 5 · Answer 16 · answered Jun 30 '19 at 11:36

1) Graphviz – download unzip in a particular place in the system (pip does not work in windows ) and include the bin folder in the path (‘set environment variables in windows’ OR) set manually in each program

import os
os.environ["PATH"] += os.pathsep + 'C:/GraphViz/bin'

2) Then put the model to plot

clf = xgb.train(params, d_train, 1000, evals=evallist, early_stopping_rounds=10)
xgb.plot_tree(clf)
plt.rcParams['figure.figsize'] = [50, 10]
plt.show()

score 5 · Answer 17 · edited Nov 24 '21 at 14:09

5

I am using windows10 , I tried installing graphwiz in program files and setting the path: Didn't worked for me

Tried

conda install -c anaconda graphviz

doesn't work.

Then tried

conda install python-graphviz

It worked, It seems our python compiler is not able to access the Graphwiz. Hence python-graphwize worked. pip install graphviz also didn't work.

edited Nov 24 '21 at 14:09

Suraj Rao

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answered Nov 24 '21 at 14:07

Kishan Kumar

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score 4 · Answer 18 · answered Dec 31 '20 at 21:26

1- first downlaod it(graphviz 2.38).

2- install org.graphviz.Graphviz-2.38-graphviz-2.38.

3- now add "C:\Program Files (x86)\Graphviz2.38\bin" and "C:\Program Files (x86)\Graphviz2.38\bin\dot.exe" to path like this video
note:in windows 8 you must use ; for path example: C:\Program Files;D:\Users;E:\file\

nono · Answer 19 · 2016-06-08T04:27:37.277

3

I had the same issue on Linux with Jupyter.

To solve it I've added the dot library to python sys.path

First: check if dot is installed,

Then:
find his path whereis dot -> /local/notebook/miniconda2/envs/ik2/bin/dot

Finally in python script : sys.path.append("/local/notebook/miniconda2/envs/ik2/bin/dot")

edited Jun 08 '16 at 04:27

answered Jun 07 '16 at 18:17

nono

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On linux I just did `sudo apt-get install graphviz` (after doing `pip install graphviz`) and after that it worked. – wordsforthewise Aug 07 '16 at 06:30
@wordsforthewise Your comment should be an answer. Solved the problem for me – Riken Shah Jan 30 '17 at 17:32
@wordsforthewise that's the answer! – SeF Nov 06 '19 at 09:28

score 3 · Answer 20 · edited May 23 '17 at 12:18

I had the same error message on Mac OS (El Capitan), using the PyCharm IDE. I had installed Graphviz using brew, as recommended in RZK's answer, and installed the graphviz python package using PyCharm (I could check Graphviz was installed correctly by trying dot -V in a terminal and getting: dot - graphviz version 2.40.1 (20161225.0304)). Yet I was still getting the error message when trying to call Graphviz from PyCharm.

I had to add the path /usr/local/bin in PyCharm options, as recommended in the answer to this question to resolve the problem.

score 3 · Answer 21 · answered Oct 31 '17 at 09:18

3

After you've installed the package (link if you haven't), add the path to dot.exe as a new system variable.

Default path is:

C:\Program Files (x86)\Graphviz2.38\bin\dot.exe

answered Oct 31 '17 at 09:18

typhon04

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i don't have this dot.exe file – Maths12 Feb 05 '21 at 18:42

score 3 · Answer 22 · answered May 28 '21 at 18:57

3

In Windows environment, use chocolately to install, it will ensure the environmental vars are set correctly.

choco install graphviz

answered May 28 '21 at 18:57

misantroop

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this worked for me. Make sure to run it in administrator mode. – john k Dec 13 '21 at 22:00

score 3 · Answer 23 · edited Feb 26 '22 at 03:48

3

When I first installed pydot and graphviz it showed me the error, but the command below worked for me:

import os
os.environ["PATH"] += os.pathsep + r'C:\Users\vivek\Downloads\graphviz-2.44.1-win32\Graphviz\bin'

edited Feb 26 '22 at 03:48

Henry Ecker

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answered Feb 26 '22 at 03:46

Vivek Saroha

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score 2 · Answer 24 · answered Feb 18 '17 at 15:10

2

First, you should use pip install, and then download another package in http://www.graphviz.org/Download_windows.php and add the install location into the environmental path, then it works.

answered Feb 18 '17 at 15:10

x2yline

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score 2 · Answer 25 · answered Jun 04 '19 at 15:59

OS Mojave 10.14., Python 3.6

Using pip install graphviz had good feedback in terminal, but lead to this error when I tried to make a graph in a Jupyter notebook. I then ran brew install graphviz, which gave an error in terminal. Then I ran conda install graphviz and the graph worked.

From @Leighton's comment: pip only gets path problem same as yours and conda only gets import error.

score 2 · Answer 26 · answered Mar 23 '20 at 08:26

2

Add graphviz to the System Path

Windows - Edit the System Environment Variables.
Choose Environment Variables.
Select Path - New
Add the Path of graphviz

Ex: C:\Users\AppData\Local\Continuum\anaconda3\Library\bin\graphviz

answered Mar 23 '20 at 08:26

Kranthi

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score 2 · Answer 27 · edited Jul 19 '21 at 22:52

try typing the following code in anaconda prompt one by one.

this worked for me.

Source: https://anaconda.org/conda-forge/python-graphviz

conda install -c conda-forge python-graphviz
conda install -c conda-forge/label/broken python-graphviz
conda install -c conda-forge/label/cf201901 python-graphviz
conda install -c conda-forge/label/cf202003 python-graphviz

Restart the kernel afterwards!

score 1 · Answer 28 · edited Oct 03 '18 at 05:16

For Linux users who don't have root access and hence can't use sudo command as suggested in other answers...

First, activate your conda virtual-environment (if you want to use one) by:

source activate virtual-env-name

Then install graphviz, even if you have already done it using pip:

conda install graphviz

then copy the result of the following command:

whereis dot

In my case, its output is:

/home/nader/anaconda2/bin/dot

and add it to your PATH variable. Just run the command below

nano ~/.bashrc

and add these lines to the end of the opened file:

PATH="/home/username/anaconda2/bin/dot:$PATH"
export PATH

now press Ctrl+O and then Ctrl+X to save and exit.

Problem should be solved by now.

Pycharm users, please note: Pycharm does not always see the PATH variable the same as your terminal. This solution does not work for Pycharm, and maybe other IDEs. But you can fix this by adding this line of code:

os.environ["PATH"] += os.pathsep + '/home/nader/anaconda2/bin'

to your python program. Do not forget to

import os

first :)

Edit: If you don't want to use conda, you can still install graphviz from here without any root permissions and add the bin folder to your PATH variable. I didn't test this.

what if `whereis dot` outputs nothing but `dot:`? I am using PyCharm on Windows to connect to Ubuntu 16.04 server and can't seem to find necessary bin folder to add `os.environ["PATH"] += os.pathsep + '...'` — bit_scientist, Mar 03 '20 at 05:26
Rather refer to this issue of mine posted [here](https://stackoverflow.com/questions/60500987/graphviz-backend-executablenotfound-failed-to-execute-dot-tpng-make-su) — bit_scientist, Mar 03 '20 at 06:07

score 1 · Answer 29 · answered Apr 24 '19 at 18:47

1.install windows package from: https://graphviz.gitlab.io/_pages/Download/Download_windows.html and download msi file

Add in Environmental variables 2. Add C:\Program Files (x86)\Graphviz2.38\bin to User path

Add C:\Program Files (x86)\Graphviz2.38\bin\dot.exe to System Path
Restart your python notebook.

It will work.

score 1 · Answer 30 · answered May 15 '20 at 19:01

#Write this on anaconda prompt in admin mode
conda install -c anaconda graphviz
conda install -c conda-forge python-graphviz
conda install -c conda-forge/label/broken python-graphviz
conda install -c conda-forge/label/cf201901 python-graphviz
conda install -c conda-forge/label/cf202003 python-graphviz

#check dot -v in window's cmd prompt
C:\WINDOWS\system32>dot -V
dot - graphviz version 2.38.0 (20140413.2041)
(this means graphviz installed successfully)

#Add path to sys and user eve variables
PATH
C:\Anaconda3\pkgs\graphviz-2.38-hfd603c8_2\Library\bin
(search bin folder of graphviz and then copy n paste path in env variables)

#Re-run all cmds in jyupter notebook
#if error occurs (less chances)
#then 
#Restart anaconda and again run all cmds in jyupter notebook
eg.
import graphviz as gp
with open("tree.dot") as f:
    dot_read=f.read()
display(gp.Source(dot_read))

score 0 · Answer 31 · edited Jan 30 '20 at 14:17

0

import os
os.environ["PATH"] += os.pathsep + "/Macintosh HD⁩/anaconda3⁩/lib⁩/⁨python3.7⁩/site-packages⁩/sphinx⁩/templates⁩/graphviz"

This solved the PATH issue on MAC for me!

edited Jan 30 '20 at 14:17

mate00

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answered Jan 30 '20 at 13:11

Antonio Piscopo

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score 0 · Answer 32 · answered Mar 01 '20 at 09:01

0

If you are not using Conda but vanilla Python, 'brew install graphviz' works.

answered Mar 01 '20 at 09:01

Bhaskar

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score 0 · Answer 33 · answered Jan 26 '21 at 22:40

Mac & Big Sur. Python 3.8.6 w/vs code. While it should have been included in diagrams package, I had to manually install graphviz.

(mymltools) ➜  infrastructure git:(master) pip list
Package    Version
---------- -------
diagrams   0.18.0
graphviz   0.13.2
Jinja2     2.11.2
MarkupSafe 1.1.1
pip        20.3.2
setuptools 51.0.0
wheel      0.36.2

Running diagrams failed. Then manually ran

pipenv install graphviz

Works like a charm.

score 0 · Answer 34 · edited Nov 18 '21 at 10:22

MACOS - Solution for Monterey

Open: Terminal
Run: pip install graphviz
Run: brew install graphviz
Close: Terminal
Open: Anaconda (Jupyter or Spyder)
Run: import os
os.environ["PATH"] += os.pathsep + "/usr/local/Cellar/graphviz/2.49.3/bin/dot"

(You'll have to run this EACH time until the bug is fixed.) The tricky part is finding the dot file. It is the location where brew installs the package. (But it should be something similar to the path that I gave.) Test by running:

import mglearn as mglearn
mglearn.plots.plot_animal_tree()

Hopefully, you are good to go now!

score 0 · Answer 35 · answered Mar 01 '22 at 11:08

0

you can use the following command in Anaconda prompt :

conda install python-graphviz

and make sure to install pm4py in Anaconda prompt :

pip install pm4py

and in the end you have to try running your python code with Anaconda propmpt.

answered Mar 01 '22 at 11:08

Ali Askari

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Curious · Answer 36 · 2023-07-18T02:35:42.970

For Mac users (this worked for me):

# not required for graphviz but required for running the below command
pip3 install pipdeptree

pip3 install graphviz
brew install graphviz

# You could include in the .bashrc or .zshrc file to make it permanent. 
# As it may not save when you close the current terminal session!
export PATH="$PATH:/usr/local/Cellar/graphviz/8.1.0/bin";

Then I can run:

pipdeptree --graph-output png > dependencies.png

FYI I used this in a virtual env with python3.8

score -1 · Answer 37 · answered Jun 21 '22 at 03:19

-1

For windows, these 2 commands work for me, in the power shell running as administrator.

pip install graphviz
choco install graphviz

answered Jun 21 '22 at 03:19

nishat rafi

1

Please make an effort to tailor your answer to the system of the asker. – dsillman2000 Jun 21 '22 at 15:24

score -2 · Answer 38 · answered Apr 24 '19 at 16:49

-2

trying doing this in python import sys !conda install --yes --prefix {sys.prefix} graphviz import graphviz

answered Apr 24 '19 at 16:49

Roli

11
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Please add more details to your answer, such as why this would fix the issue – Deiv Apr 24 '19 at 16:52

"RuntimeError: Make sure the Graphviz executables are on your system's path" after installing Graphviz 2.38

38 Answers38

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