mamba init & new Mac #24688

joe61vette · 2023-06-14T18:35:04Z

joe61vette
Jun 14, 2023

Hello:

I just began the install process on a new Mac with Ventura 13.4. All works well until the "mamba activate moose" step. Then I get the
"Run 'mamba init' to be able to run mamba activate/deactivate
and start a new shell session. Or use conda to activate/deactivate."
message. Note that this also happens for a "testing" environment as per the troubleshooting instructions.

I have deleted and re-installed mamba a number of time with the same results. I pasted the following into my .zshrc file:

`# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/Users/joe/mambaforge3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/Users/joe/mambaforge3/etc/profile.d/conda.sh" ]; then
        . "/Users/joe/mambaforge3/etc/profile.d/conda.sh"
    else
        export PATH="/Users/joe/mambaforge3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

mamba activate moose

export HOST=$(hostname)`

My .condarc file is

`channels: [https://conda.software.inl.gov/public, conda-forge]

If I do a 'mamba info', I get:

(base) ~ % mamba info

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (1.4.1) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████


     active environment : base
    active env location : /Users/joe/mambaforge3
            shell level : 1
       user config file : /Users/joe/.condarc
 populated config files : /Users/joe/mambaforge3/.condarc
                          /Users/joe/.condarc
          conda version : 23.1.0
    conda-build version : not installed
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=arm64
                          __osx=13.4=0
                          __unix=0=0
       base environment : /Users/joe/mambaforge3  (writable)
      conda av data dir : /Users/joe/mambaforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.software.inl.gov/public/osx-arm64
                          https://conda.software.inl.gov/public/noarch
                          https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /Users/joe/mambaforge3/pkgs
                          /Users/joe/.conda/pkgs
       envs directories : /Users/joe/mambaforge3/envs
                          /Users/joe/.conda/envs
               platform : osx-arm64
             user-agent : conda/23.1.0 requests/2.28.2 CPython/3.10.10 Darwin/22.5.0 OSX/13.4
                UID:GID : 501:20
             netrc file : None
           offline mode : False

(base) ~ %

Any suggestions? Is there some way to completely begin anew? Or does this have to do with Mac OS 13.4?

Thanks,
Joe Kelly

Answered by milljm

Jun 15, 2023

OOooo. I just realized I have something very important in my initialization profile that you do not:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/Users/milljm/mambaforge3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/Users/milljm/mambaforge3/etc/profile.d/conda.sh" ]; then
        . "/Users/milljm/mambaforge3/etc/profile.d/conda.sh"
    else
        export PATH="/Users/milljm/mambaforge3/bin:$PATH"
    fi
fi
unset __conda_setup

if [ -f "/Users/milljm/mambaforge3/etc/profile.d/mamba.sh" ]; then    <-- where did
    . "/Users/milljm/mambaforge3/etc/profile.d/mam…

View full answer

GiudGiud · 2023-06-14T18:44:46Z

GiudGiud
Jun 14, 2023
Collaborator

Hello
So the issue that it s always asks for init even though you've done mamba init closed the terminal and re-opened already

You are working with zsh not bash right?

4 replies

joe61vette Jun 14, 2023
Author

Hi Guillaume. Yes. I am working on zsh. And it continually keeps asking for init.

GiudGiud Jun 14, 2023
Collaborator

The mamba activate moose in your .zshrc also asks for an init?
If there is anything derailing or returning early from the .zshrc that could prevent the initialize part from running

@milljm

joe61vette Jun 14, 2023
Author

I get:

(base) ~ % mamba activate moose
Run 'mamba init' to be able to run mamba activate/deactivate
and start a new shell session. Or use conda to activate/deactivate.

and

(base) ~ % mamba init

              __    __    __    __
             /  \  /  \  /  \  /  \
            /    \/    \/    \/    \

███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ ____
/ / _/ _/ _/ \ o _,
/ / ___/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝

    mamba (1.4.1) supported by @QuantStack

    GitHub:  https://github.com/mamba-org/mamba
    Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

no change /Users/joe/mambaforge3/condabin/conda
no change /Users/joe/mambaforge3/bin/conda
no change /Users/joe/mambaforge3/bin/conda-env
no change /Users/joe/mambaforge3/bin/activate
no change /Users/joe/mambaforge3/bin/deactivate
no change /Users/joe/mambaforge3/etc/profile.d/conda.sh
no change /Users/joe/mambaforge3/etc/fish/conf.d/conda.fish
no change /Users/joe/mambaforge3/shell/condabin/Conda.psm1
no change /Users/joe/mambaforge3/shell/condabin/conda-hook.ps1
no change /Users/joe/mambaforge3/lib/python3.10/site-packages/xontrib/conda.xsh
no change /Users/joe/mambaforge3/etc/profile.d/conda.csh
modified /Users/joe/.bash_profile

==> For changes to take effect, close and re-open your current shell. <==

Added mamba to /Users/joe/.bash_profile

==> For changes to take effect, close and re-open your current shell. <==

(base) ~ %

Note that it added mamba to bash. Does that make a difference?

Then I close terminal window & open another.

Last login: Wed Jun 14 14:02:00 on ttys001
Run 'mamba init' to be able to run mamba activate/deactivate
and start a new shell session. Or use conda to activate/deactivate.

(base) ~ %

Note there is a 'mamba activate moose' in my .zshrc file.

GiudGiud Jun 14, 2023
Collaborator

can you paste a screenshot of a fresh new terminal?

mamba thinks you are using bash right now.

joe61vette · 2023-06-14T19:05:16Z

joe61vette
Jun 14, 2023
Author

I killed terminal and then relaunched it. The screenshot is attached.

22 replies

milljm Jun 15, 2023
Maintainer

I am able to replicate your issue when I do the following:

(base) env -i zsh -f   # starts a new zsh environment, clean of any profiles
INL618984%
INL618984% junk="$('/Users/milljm/mambaforge3/bin/conda' 'shell.zsh' 'hook')"
INL618984% eval ${junk}
(base) INL618984%
(base) INL618984% mamba activate moose
Run 'mamba init' to be able to run mamba activate/deactivate
and start a new shell session. Or use conda to activate/deactivate.

At least I have something I can play around with on my own.

milljm Jun 15, 2023
Maintainer

Okay, so when mamba is not a function, it calls the binary (well executable script) mamba within your PATH. Which has that message hard-coded:

# Main entry point!
def main(*args, **kwargs):
    # Set to false so we don't allow uploading our issues to conda!
    context.report_errors = False

    from conda.common.compat import ensure_text_type
    if "activate" in sys.argv or "deactivate" in sys.argv:
        print(
            "Run 'mamba init' to be able to run mamba activate/deactivate\n"
            "and start a new shell session. Or use conda to activate/deactivate.\n",
            file=sys.stderr,
        )
        return sys.exit(-1)

I suspect your mamba is not a function then? Can you check?

(base) INL618984% type mamba
mamba is /Users/milljm/mambaforge3/bin/mamba

as opposed to what it wants:

❯ type mamba
mamba is a shell function from /Users/milljm/mambaforge3/etc/profile.d/mamba.sh

I am confused a bit on how Mamba is initialized as a function (er, or rather how it is not initialized). When I figure that out, I'll post again.

milljm Jun 15, 2023
Maintainer

Indeed...

(base) INL618984% source /Users/milljm/mambaforge3/etc/profile.d/mamba.sh
(base) INL618984% type mamba
mamba is a shell function from /Users/milljm/mambaforge3/etc/profile.d/mamba.sh
(base) INL618984% mamba activate moose
(moose) INL618984%

So why is your mamba.sh not being 'sourced' properly when you activate the base environment.

milljm Jun 15, 2023
Maintainer

OOooo. I just realized I have something very important in my initialization profile that you do not:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/Users/milljm/mambaforge3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/Users/milljm/mambaforge3/etc/profile.d/conda.sh" ]; then
        . "/Users/milljm/mambaforge3/etc/profile.d/conda.sh"
    else
        export PATH="/Users/milljm/mambaforge3/bin:$PATH"
    fi
fi
unset __conda_setup

if [ -f "/Users/milljm/mambaforge3/etc/profile.d/mamba.sh" ]; then    <-- where did
    . "/Users/milljm/mambaforge3/etc/profile.d/mamba.sh"              <-- this come
fi                                                                    <-- from??
# <<< conda initialize <<<

I have the all-important mamba source. With that said, I am willing to bet you can use conda activate instead of mamba activate.

I also think I know how this came to be 😄

When you install Conda or Mamba, it will detect the presence of:

# >>> conda initialize >>>
anything in between these identifiers 
# <<< conda initialize <<<

already in your profile and not modify the profile again. So this means you may have had a non-mamba install at some point?

Answer selected by joe61vette

joe61vette Jun 15, 2023
Author

I add these 2 lines to my .zshrc and all is well.

if [ -f "/Users/joe/mambaforge3/etc/profile.d/mamba.sh" ]; then
. "/Users/joe/mambaforge3/etc/profile.d/mamba.sh"
fi

It is likely that I had copied a .zshrc file from another computer before installing mamba. So the 'condo initialize' stuff got skipped. Why those lines are necessary on this computer and not the other one... That will remain a mystery to me.

THANKS so much for the help. It is greatly appreciated !

joe61vette Jun 15, 2023
Author

This is what I got for mamba type:

moose) ~ % type mamba
mamba is a shell function from /Users/joe/mambaforge3/etc/profile.d/mamba.sh

milljm Jun 15, 2023
Maintainer

Now that its a function, mamba activate should work :)

Cheers! Thanks for reporting the issue. I learned some things.

jayant-yadav · 2024-05-10T10:41:19Z

jayant-yadav
May 10, 2024

I wrecked my brain for days on this. Until I stumbled upon this answer
All I had to do was to mamba init zsh because it needed shell name.
I am using Intel MacBook Pro.

0 replies

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mamba init & new Mac #24688

joe61vette Jun 14, 2023

Replies: 3 comments · 26 replies

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