Troubleshooting#

Navigator error on start up#

This is often the result of a corrupted .condarc file. To resolve, delete the .condarc file and restart Navigator.

Find the .condarc file.

In Anaconda Prompt or the terminal, enter the command conda info. The output will tell you the location of your .condarc file(s). You can also search for “.condarc” on your computer.

The .condarc file is frequently found in:
- macOS: /Users/<USERNAME>
- Linux: ~/.condarc
- Windows: C:\\Users\\<USERNAME>
Optional: Save custom configurations.

If you had custom configuration in your .condarc file before it was corrupted, save the information to add that configuration back to the new file.
Delete the .condarc file.
Restart Navigator.

Issues launching or initializing#

If you are having problems launching Anaconda Navigator, follow these steps.

If you cannot launch the Anaconda Navigator desktop app, you can still launch it from the terminal or an Anaconda Prompt with anaconda-navigator.

Permissions issues#

If you have permissions issues, there may be a problem with the licenses directory, .continuum. Open a terminal or Anaconda Prompt and delete the .continuum directory. Run rm -rf ~/.continuum on macOS and Linux and rd /s .continuum on Windows.

Then relaunch Navigator from the desktop app, terminal, or Anaconda Prompt.

Other options#

If removing the licenses directory does not resolve the issue, manually update Navigator from a terminal or an Anaconda Prompt:

conda update anaconda-navigator

If you have updated Navigator and still have problems, remove Anaconda Navigator, then reinstall from the terminal or Anaconda Prompt:

conda remove anaconda-navigator
conda install anaconda-navigator

If none of the above work, please reset the Anaconda Navigator configuration back to default values:

anaconda-navigator --reset

PermissionError on macOS Catalina#

MacOS Catalina users may experience permission errors where the system does not prompt you for permission to folders requiring access.

First, update Navigator.

conda update anaconda-navigator

Once updated, have Navigator generate the permissions prompt by launching Spyder and running the following in the console:

import os
os.listdir('<DIRECTORY>')
# Replace <DIRECTORY> with the folder you need access to.

Access denied error#

This is caused by a lock file that sometimes gets stuck and isn’t removed when it should be.

In Anaconda Prompt or a terminal, run:

conda update conda
conda update anaconda-navigator
conda update navigator-updater
anaconda-navigator --reset

The last command is the key to fixing the issue, as it removes the lock file causing the problem.

Navigator buttons are missing#

If your Navigator buttons are missing, try the following:

Run Update Index from the Environments page of Navigator.
Quit and restart Navigator.

If it’s still broken, confirm that your .condarc file is not corrupt. Specifically confirm that your channel settings contain “defaults”.
If it’s still broken, try running conda search python from the command line. This will download a fresh copy of the repodata, which should resolve the problem.
If none of the above options work, open an issue detailing the error.

Navigator ignores the “Ok, and don’t show again” option on the help Anaconda improve pop up#

After starting Navigator, a pop up appears asking if you’d like to provide anonymized usage information to Anaconda. If you select “Okay, and don’t show again” and the pop up appears again the next time you start Navigator, it may be due to a privilege conflict.

Specifically, this can occur when Navigator was installed by a user with Administrator privileges, but you are using it as a regular user without the Administrator privileges. The pop up continues to appear because you do not have permission to change the pop up box setting.

To resolve this, switch to using an account with Administrator privileges and select the “Ok, and don’t show again” option in the pop up box. This will apply to all user accounts.

Alternatively, edit the show_startup field in the .anaconda/navigator/anaconda-navigator.ini configuration file so that it is False. If show_startup = True, you will continue to see the pop up box.

Trouble logging in to the Anaconda Server connection in Navigator#

If you are having issues logging in or know you’re logged in but cannot interact with Anaconda Server, try the following steps:

Set logged_api_url, anaconda_server_token, and anaconda_server_token_id in the Navigator config file (anaconda-navigator.ini) to None.

Note

The token and token ID config variable names have been updated from team_edition_token to anaconda_server_token and team _edition_token_id to anaconda_server_token_id as of Version 2.4.0. If you downgrade your Navigator application to a version older than 2.3.0, you will need to manually change these variable names back to their older versions within your anaconda-navigator.ini file.
Remove channel_alias from the conda configuration file (.condarc).
Try signing in again.

VS Code is not appearing on my Anaconda Navigator home tab#

Anaconda Navigator displays and launches VS Code, and many other applications, through that application’s executable file. VS Code’s installation should have placed the executable in a specific directory where Anaconda Navigator is programmed to look. For example:

Windows User-Only Installation: C:\\Users\\User\\AppData\\Local\\Programs\\Microsoft VS Code

Windows System-Wide Installation: C:\\Program Files\\Microsoft VS Code

Linux-64: /usr/share/code

macOS: /Applications

Reinstall VS Code to ensure that executable is installed in the default location.

Close Anaconda Navigator.
Uninstall (if necessary) and reinstall VS Code.

Note

On macOS, make sure the VS Code application is moved from your Downloads folder to your Applications folder.
Re-open Anaconda Navigator.

Another option, if you have installed VS Code to a different location than the default, is to edit VS Code’s path in your Anaconda Navigator user preferences.

Open the Anaconda Navigator Preferences dialog from the top menu bar (such as File > Preferences or Anaconda Navigator > Preferences).
Scroll down to the VS Code path setting.
Enter the path to the installation of VS Code you would like Anaconda Navigator to use. This may be similar to the examples above, especially if you have a user-specific installation you would rather use over your system-wide installation.

Note

You do not need to enter the name of the executable file itself. Just the path to the folder that contains that file.
Close and reopen Anaconda Navigator.

Anaconda Navigator fails to start and gives Permission denied error#

After installation, Anaconda Navigator may fail to start and give you a “Permission denied” error on the anaconda-client configuration file (/.continuum/anaconda-client/config.yaml).

Cause#

This error is likely due to anaconda-client being installed with admin rights. This will lead to incorrect user permissions for the anaconda-client config file.

Solution#

You can do a few things to solve this. They are listed from most straightforward to most complex.

Delete your .continuum folder

Back up your .config.yaml file to a different location.
Delete your .continuum folder.
Start Navigator again.
Copy your saved .config.yaml file back into /.continuum/anaconda-client.

Uninstall and reinstall without admin privileges

Uninstall Anaconda and then reinstall Anaconda without admin privileges.

Manually change the .continuum folder’s user permissions

You will need administrator privileges to do this.

To change user permissions on Windows:

Search for “powershell”.
Right-click the Windows PowerShell app and select Run as administrator.

Run the following command:

#Replace <USERNAME> with your username
icacls C:\Users\<USERNAME>\.continuum /grant:r <USERNAME>:(i,f) /t

To change user permissions on macOS or Linux

Open your terminal application.
Run the following command:
```
sudo chmod 766 /.continuum
```

Navigator gives ‘Email verification failed’ error 403#

Users with unverified Anaconda.org email addresses can no longer access the API that Navigator and Anaconda Client use to communicate with Anaconda.org. Navigator 2.5.0+ now catches this error and logs you out of your Anaconda.org connection. To connect to Anaconda.org again through Navigator, update your Navigator version or verify your Anaconda.org account.

Verify your anaconda.org account#

To fully resolve the issue, we recommend verifying your account on Anaconda.org:

Log in to your Anaconda.org account.
If your email is unverified, you will be prompted to verify it.
Click Resend Confirmation Email.
Follow the instructions in the email you receive to complete the verification process.

This issue will be resolved in the next Navigator release.

CentOS 7: Orange3 fails to launch after installation#

Cause#

In the CentOS 7 Linux operating system, Orange3 is missing some graphics libraries required by Qt, a framework that Orange Canvas requires to work.

These missing dependencies cause an error when starting Navigator: “Could not load the Qt platform plugin “xcb” in “” even though it was found. This application failed to start because no Qt platform plugin could be initialized.”

Solution#

Open a terminal application.

Install the missing system libraries and run updates by running the following commands:

sudo yum install xcb-util-wm xcb-util-image xcb-util-keysyms xcb-util-renderutil
sudo yum update

Once these libraries are installed and updated, Orange3 should launch correctly on CentOS 7 and the above error should no longer appear when opening Navigator with Orange3 installed.