anaconda conda: error: argument command: invalid choice when trying to update packages

Question

I am using ubuntu 18 with anaconda for python 3.6 and trying to update packages, when I try to do so using

conda update --all 

I am getting this error

conda: error: argument command: invalid choice: '/home/user/anaconda3/bin/conda'

I tried so solve it like explained in this github issue

using

$ conda update anaconda-navigator
$ conda update navigator-updater

But getting the same error. I tried adding -c conda-forge to all the commands And tried using conda update anaconda conda upgrade anaconda

and getting the same error all the time.

Here is my github issue on this

Thanks!

update: even when trying to use this to install anaconda-clean and removing anaconda, I am getting the same error when trying to install conda-clean that should help me remove anaconda from my machine

Answer 1

The issue of Conda yielding unexpected errors across different environments is well-known. Often, the default settings clash with one's own, or if self-configured, an incorrect path may have been set in one's shell configuration file (in my case, for instance, the ~/.zshrc file).

One could meticulously analyze the causes, set the correct path, and then restart the shell (for zsh, this would be executed via zsh -l).

Quick solution

However, if you're in a hurry and wish to make all the necessary configurations later, a more expedient solution exists on Linux-based systems; you can simply try the following:

source activate <env-name>

Understanding the issues

Upon initializing Conda, it would also be prudent to specify the name of one's own shell, such as

conda init zsh 

Subsequently, a list of system modifications will be displayed:

no change     /opt/homebrew/anaconda3/condabin/conda
no change     /opt/homebrew/anaconda3/bin/conda
no change     /opt/homebrew/anaconda3/bin/conda-env
no change     /opt/homebrew/anaconda3/bin/activate
no change     /opt/homebrew/anaconda3/bin/deactivate
no change     /opt/homebrew/anaconda3/etc/profile.d/conda.sh
no change     /opt/homebrew/anaconda3/etc/fish/conf.d/conda.fish
no change     /opt/homebrew/anaconda3/shell/condabin/Conda.psm1
no change     /opt/homebrew/anaconda3/shell/condabin/conda-hook.ps1
no change     /opt/homebrew/anaconda3/lib/python3.11/site-packages/xontrib/conda.xsh
no change     /opt/homebrew/anaconda3/etc/profile.d/conda.csh
modified /Users/<username>/.zshrc # <--- ADDITONAL CHANGES

Upon inspection here, one would discover this entry.

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/homebrew/anaconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/opt/homebrew/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/opt/homebrew/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/opt/homebrew/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

After restarting one's own shell (as previously mentioned, with zsh -l where -l stands for load), the command

conda activate <env-name> 

should then operate as desired.

In conclusion, a brief summary:

1. Initialisation

conda init <shell-name> # e.g., zsh or bash

2. Apply the changes by restarting the terminal.

If it is zsh, then

zsh -l

3. Create a new environment for a certain python version

conda create --name <env-name> python=3 

4. Check if the environment is already created

conda env list 

An example would be:

base                     /opt/homebrew/anaconda3
codellama             *  /opt/homebrew/anaconda3/envs/codellama
llama2                   /opt/homebrew/anaconda3/envs/llama2

The * indicates that codellama is currently active

5. Active the environment

conda activate <env-name>

This should function without any issues.

Answer 2

I had the same issue, just run

conda init

Saved me after one whole hour of troubleshooting. Turns out my C:\Users\**\miniconda3\Scripts\activate and C:\Users\**\miniconda3\Scripts\deactivate weren't updated.