Problem with permissions in macOS Catalina #11387

luismiguells · 2019-10-21T17:27:42Z

Actual Behavior

I upgrade macOS to Catalina. The problem is that now, I can't read any file. I tried to reinstall Anaconda but it doesn't work. I also reinstall the OS. When I run gives me this error:

PermissionError: [Errno 1] Operation not permitted: '/Users/luismiguells/...'

Steps to Reproduce

I upgrade to macOS Catalina and I made a clean install with the command line installer.

Anaconda or Miniconda version:

Anaconda3

Operating System:

macOS Catalina

The text was updated successfully, but these errors were encountered:

csoja · 2019-10-21T17:44:35Z

Please see this blog post for tips on Anaconda & Catalina: https://www.anaconda.com/how-to-restore-anaconda-after-macos-catalina-update/

luismiguells · 2019-10-21T19:06:29Z

Please see this blog post for tips on Anaconda & Catalina: https://www.anaconda.com/how-to-restore-anaconda-after-macos-catalina-update/

I already did that. The problem is I made a clean installation and it doesn't work.

csoja · 2019-10-21T20:13:14Z

It says "PermissionError" - do you have the appropriate permissions to access that directory in the terminal where you are running the command line installer? In other words, can you read/write/execute in the terminal in that directory separate from anything to do with the Anaconda installer.

luismiguells · 2019-10-21T20:19:11Z

It says "PermissionError" - do you have the appropriate permissions to access that directory in the terminal where you are running the command line installer? In other words, can you read/write/execute in the terminal in that directory separate from anything to do with the Anaconda installer.

I already install Anaconda. The error comes when I execute a script.

forrestwaters · 2019-10-22T18:51:45Z

This seems to be a different problem introduced with MacOS Catalina where certain user folders are protected (Desktop/Documents/Downloads). According to Apple, your system is supposed to prompt you to request permission to those folders when access is needed. However that doesn't seem to apply to non-MacOS apps like the python interpreter, or shell commands run via terminal (for what it's worth, this problem also happens for the default python and terminal included with MacOS).

One workaround you could try:

With Spyder open, hit the open folder button in the top left corner (cmd + o). Once there, navigate to the folder that you need access to and try to open a file (in your case the Documents folder). Once that is done, re-run your code and see if the permissions error is still there.

Would you be willing to try that and let us know if it solves your problem?

MarcosCarreira · 2019-10-23T09:52:33Z

I had similar problems, installed the new version, but Jupyter Lab cannot access Desktop and Documents if launched from the Navigator; if launched from the terminal the authorization question pops up and it works; so now Spyder, Notebook and VS Code are ok, but Jupyter Lab still needs to launched by the terminal.

DanilZherebtsov · 2019-10-24T14:43:54Z

This seems to be a different problem introduced with MacOS Catalina where certain user folders are protected (Desktop/Documents/Downloads). According to Apple, your system is supposed to prompt you to request permission to those folders when access is needed. However that doesn't seem to apply to non-MacOS apps like the python interpreter, or shell commands run via terminal (for what it's worth, this problem also happens for the default python and terminal included with MacOS).

One workaround you could try:

With Spyder open, hit the open folder button in the top left corner (cmd + o). Once there, navigate to the folder that you need access to and try to open a file (in your case the Documents folder). Once that is done, re-run your code and see if the permissions error is still there.

Would you be willing to try that and let us know if it solves your problem?

I've tried what you are proposing. When using the open button I can see and open any script located in that folder. But when I try to:

navigate to the Documents folder via Spyder File explorer, the folder is empty
navigate to the Documents folder from IPython console - I get a PermissionError

Documents folder via "Open" button:

Documents folder via File explorer:

IPython console command:

luismiguells · 2019-10-24T16:41:16Z

I run the command spyder or sudo spyder in the terminal. It helps me to avoid the problem, but when I run Spyder from Anaconda-Navigator, the problem stills.

allenea · 2019-10-31T16:28:00Z

For me too. Have no problem with running from the command line but cannot run on Spyder from Anaconda-Navigator.

The issue definitely has to do with the path manager. I was able to get one of my programs running by manually adding the path to PATHMANAGER and it worked. I since removed it. Restarted everything and it still remembers it. However I also set Documents/Downloads/Desktop (more generalized paths) and those do not work. No other program outside of the folder which my imports were located can be found. That now includes modules like Numpy.

That was only a partial fix... I think I have a good one. So I reinstalled a 4th time. Using the command line installer. But this time I made sure to delete the ~/.<fille/folder> related to python. iPython, Spyder, conda, anaconda, bash_profile, etc. After reinstalling to the /User/<your_home folder>/ (not OPT). At this time I also switched to zsh so conda init zsh. Restart your terminal window. Open up Anaconda/Spyder. Then I installed your packages. There may still be some problems at this point if you look at the ~/.spyder-py3 there should be a directory called workingdir. This will hold all the valid paths. So when you run your program make sure it's "the default working directory is the directory where the file is being executed from" and "console directory is the current working directory". Then I started to run on my various programs. Expanded outwards. Now I am having no troubles with permissions or running in spyder or terminal. I have access to all modules.

azeezx · 2019-11-03T17:11:20Z

Solved:

What I did I create a new folder I call it 'dev' in my user folder and moved all my files & folders in there, then the permission error disappeared.

Hope this will help you as well.

DanilZherebtsov · 2019-11-04T14:00:53Z

Solved:

What I did I create a new folder I call it 'dev' in my user folder and moved all my files & folders in there, then the permission error disappeared.

Hope this will help you as well.

I did the same and it does solve the problem indeed, but not quite. For example you download some data into the Downloads folder and then use that location to import data via Spyder (pd.read_csv('...') and here again you have the same problem. First you have to move those downloads elsewhere then you can import them.

I consider this a temporary workaround...

dsimonovic · 2019-12-02T13:34:57Z

I have granted "Full Disk Access" to Terminal and sh in Privacy settings and it worked. Details are here:
http://osxdaily.com/2018/10/09/fix-operation-not-permitted-terminal-error-macos/

forrestwaters · 2019-12-06T16:18:18Z

I have uploaded a new Navigator package for OSX. Now when attempting to access these folders you should receive a prompt the first time requesting permission. You can update by running this from the terminal in the environment where you have anaconda-navigator installed:

conda update anaconda-navigator

Once updated, the easiest way I've found to generate the permissions prompt for Navigator for the first time is to open Spyder and run something like this in the console (can replace Desktop with Downloads/Documents folder depending which you need access to):

import os
os.listdir('Desktop')

MarcosCarreira · 2019-12-06T21:21:11Z

It works! I had a new computer with the same problem, updated navigator and the questions are asked for access to Anaconda-Navigator.app both in Spyder and JupyterLab (it asks again on each though).
Thanks!

forrestwaters · 2019-12-06T22:35:15Z

Thanks for testing @MarcosCarreira , glad that worked.

DanilZherebtsov · 2019-12-13T17:04:01Z

I have uploaded a new Navigator package for OSX. Now when attempting to access these folders you should receive a prompt the first time requesting permission. You can update by running this from the terminal in the environment where you have anaconda-navigator installed:
conda update anaconda-navigator
Once updated, the easiest way I've found to generate the permissions prompt for Navigator for the first time is to open Spyder and run something like this in the console (can replace Desktop with Downloads/Documents folder depending which you need access to):
import os
os.listdir('Desktop')

Thanks for the fix. It does work as described. One thing though: it keeps asking for the permission over and over. So after the first permission is granted, it does access the folder, but keeps asking if again I try to access the same folder... This is all within a single Spyder (python console) session. Any thoughts on that?

MarcosCarreira · 2019-12-18T21:35:30Z

Unfortunately the new Catalina update broke it - I decided to not use these folders for any code whatsoever.

DanilZherebtsov · 2019-12-24T12:01:53Z

Can't believe that it will stay like that! Anyone please update if you will find a fix for that.

mhadi813 · 2020-02-03T05:23:41Z

I have granted "Full Disk Access" to Terminal and sh in Privacy settings and it worked. Details are here:
http://osxdaily.com/2018/10/09/fix-operation-not-permitted-terminal-error-macos/

it worked for me. Thanks!
I added python3, terminal and bunch of other jupyter apps

keslingmj · 2020-02-26T20:54:54Z

This seems to be a different problem introduced with MacOS Catalina where certain user folders are protected (Desktop/Documents/Downloads). According to Apple, your system is supposed to prompt you to request permission to those folders when access is needed. However that doesn't seem to apply to non-MacOS apps like the python interpreter, or shell commands run via terminal (for what it's worth, this problem also happens for the default python and terminal included with MacOS).

One workaround you could try:

With Spyder open, hit the open folder button in the top left corner (cmd + o). Once there, navigate to the folder that you need access to and try to open a file (in your case the Documents folder). Once that is done, re-run your code and see if the permissions error is still there.

Would you be willing to try that and let us know if it solves your problem?

This worked for me. I should add that simply navigating to the folder in question is insufficient to get Anaconda's Spyder to recognize that directory as readable by macOS Catalina. I needed to create a text file in the directory in question and actually open it in Spyder. After that, any file in that directory could be read. (My other files aren't actually .txt files or .py files, so I couldn't open them in Spyder.)

Simsimasel · 2021-08-19T20:23:16Z

Hello i have anaconda- navigator problem, it doesn't start. i tried to remove .anaconda once i launche the navigator the .anaconda folder restore.
thank you for helping me : macos sierre 10.12.6
active environment : base
active env location : /Users/utilisateur/anaconda3
shell level : 1
user config file : /Users/utilisateur/.condarc
populated config files :
conda version : 4.10.3
conda-build version : 3.21.4
python version : 3.8.8.final.0
virtual packages : __osx=10.12.6=0
__unix=0=0
__archspec=1=x86_64
base environment : /Users/utilisateur/anaconda3 (writable)
conda av data dir : /Users/utilisateur/anaconda3/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /Users/utilisateur/anaconda3/pkgs
/Users/utilisateur/.conda/pkgs
envs directories : /Users/utilisateur/anaconda3/envs
/Users/utilisateur/.conda/envs
platform : osx-64
user-agent : conda/4.10.3 requests/2.25.1 CPython/3.8.8 Darwin/16.7.0 OSX/10.12.6
UID:GID : 501:20
netrc file : None
offline mode : False

packages in environment at /Users/utilisateur/anaconda3:

Simsimasel · 2021-08-20T12:42:10Z

hello i found my problem i had to go to "https://docs.anaconda.com/anaconda/install/#old-os" and choose the right version to my mac os on anaconda archive "https://repo.anaconda.com/archive/"

good luck.

This was referenced Oct 22, 2019

Anaconda 2019/10 Spyder does not see the Documents folder Mac #11377

Closed

Unable to read files or import modules outside of the working directory #11378

Closed

csoja mentioned this issue Oct 23, 2019

The documents,dekstop and downloads folder can not be accessed in Jupyterlab MacOS Catalina #11350

Closed

csoja added the type-bug label Nov 22, 2019

forrestwaters closed this as completed Dec 6, 2019

This was referenced Feb 23, 2020

OSERROR -1743 with Jupyter on macOS xlwings/xlwings#1266

Closed

OS error: -1743 xlwings/xlwings#1262

Closed

joelostblom mentioned this issue Mar 21, 2020

The documents,dekstop and downloads folder can not be accessed in Jupyterlab MacOS Catalina BME1478H/Fall2022class#244

Closed

jcohenadad mentioned this issue Nov 10, 2020

Activating conda env doesn't override user's pyenv during install_sct spinalcordtoolbox/spinalcordtoolbox#3029

Closed

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Problem with permissions in macOS Catalina #11387

Problem with permissions in macOS Catalina #11387

luismiguells commented Oct 21, 2019 •

edited

csoja commented Oct 21, 2019

luismiguells commented Oct 21, 2019 •

edited

csoja commented Oct 21, 2019

luismiguells commented Oct 21, 2019

forrestwaters commented Oct 22, 2019 •

edited

MarcosCarreira commented Oct 23, 2019

DanilZherebtsov commented Oct 24, 2019

luismiguells commented Oct 24, 2019 •

edited

allenea commented Oct 31, 2019 •

edited

azeezx commented Nov 3, 2019

DanilZherebtsov commented Nov 4, 2019

dsimonovic commented Dec 2, 2019 •

edited

forrestwaters commented Dec 6, 2019

MarcosCarreira commented Dec 6, 2019

forrestwaters commented Dec 6, 2019

DanilZherebtsov commented Dec 13, 2019

MarcosCarreira commented Dec 18, 2019

DanilZherebtsov commented Dec 24, 2019

mhadi813 commented Feb 3, 2020 •

edited

keslingmj commented Feb 26, 2020

Simsimasel commented Aug 19, 2021

Simsimasel commented Aug 20, 2021

Problem with permissions in macOS Catalina #11387

Problem with permissions in macOS Catalina #11387

Comments

luismiguells commented Oct 21, 2019 • edited

Actual Behavior

Steps to Reproduce

Anaconda or Miniconda version:

Operating System:

csoja commented Oct 21, 2019

luismiguells commented Oct 21, 2019 • edited

csoja commented Oct 21, 2019

luismiguells commented Oct 21, 2019

forrestwaters commented Oct 22, 2019 • edited

MarcosCarreira commented Oct 23, 2019

DanilZherebtsov commented Oct 24, 2019

luismiguells commented Oct 24, 2019 • edited

allenea commented Oct 31, 2019 • edited

azeezx commented Nov 3, 2019

DanilZherebtsov commented Nov 4, 2019

dsimonovic commented Dec 2, 2019 • edited

forrestwaters commented Dec 6, 2019

MarcosCarreira commented Dec 6, 2019

forrestwaters commented Dec 6, 2019

DanilZherebtsov commented Dec 13, 2019

MarcosCarreira commented Dec 18, 2019

DanilZherebtsov commented Dec 24, 2019

mhadi813 commented Feb 3, 2020 • edited

keslingmj commented Feb 26, 2020

Simsimasel commented Aug 19, 2021

packages in environment at /Users/utilisateur/anaconda3:

Name Version Build Channel

Simsimasel commented Aug 20, 2021

luismiguells commented Oct 21, 2019 •

edited

luismiguells commented Oct 21, 2019 •

edited

forrestwaters commented Oct 22, 2019 •

edited

luismiguells commented Oct 24, 2019 •

edited

allenea commented Oct 31, 2019 •

edited

dsimonovic commented Dec 2, 2019 •

edited

mhadi813 commented Feb 3, 2020 •

edited