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Homebrew M1 conda update -n base conda: The environment is inconsistent, please check the package plan carefully #325

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nyngwang opened this issue Jun 26, 2022 · 26 comments
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bug Something isn't working

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@nyngwang
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Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

Collecting package metadata (current_repodata.json): done
Solving environment: -
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - conda-forge/noarch::requests==2.27.1=pyhd8ed1ab_0
  - conda-forge/osx-arm64::brotlipy==0.7.0=py39hb18efdd_1004
  - conda-forge/osx-arm64::setuptools==62.3.2=py39h2804cbe_0
  - conda-forge/noarch::six==1.16.0=pyh6c4a22f_0
  - conda-forge/noarch::charset-normalizer==2.0.12=pyhd8ed1ab_0
  - conda-forge/osx-arm64::python==3.9.13=hc596b02_0_cpython
  - conda-forge/osx-arm64::sqlite==3.38.5=h40dfcc0_0
  - conda-forge/noarch::urllib3==1.26.9=pyhd8ed1ab_0
  - conda-forge/noarch::wheel==0.37.1=pyhd8ed1ab_0
  - conda-forge/osx-arm64::readline==8.1=hedafd6a_0
  - conda-forge/osx-arm64::ruamel_yaml==0.15.80=py39h9eb174b_1007
  - conda-forge/noarch::colorama==0.4.4=pyh9f0ad1d_0
  - conda-forge/osx-arm64::cffi==1.15.0=py39h52b1de0_0
  - conda-forge/noarch::pyopenssl==22.0.0=pyhd8ed1ab_0
  - conda-forge/noarch::tqdm==4.64.0=pyhd8ed1ab_0
  - conda-forge/noarch::pip==22.1.2=pyhd8ed1ab_0
  - conda-forge/noarch::idna==3.3=pyhd8ed1ab_0
  - conda-forge/osx-arm64::pysocks==1.7.1=py39h2804cbe_5
  - conda-forge/osx-arm64::pycosat==0.6.3=py39hb18efdd_1010
  - conda-forge/osx-arm64::cryptography==37.0.2=py39h4cb6239_0
  - conda-forge/osx-arm64::conda==4.12.0=py39h2804cbe_0
  - conda-forge/osx-arm64::python_abi==3.9=2_cp39
  - conda-forge/osx-arm64::conda-package-handling==1.8.1=py39hb18efdd_1
  - conda-forge/osx-arm64::certifi==2022.5.18.1=py39h2804cbe_0
  - conda-forge/noarch::pycparser==2.21=pyhd8ed1ab_0
done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 4.13.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: /opt/homebrew/Caskroom/miniforge/base

  added / updated specs:
    - conda


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2022.6.15  |       h4653dfc_0         149 KB  conda-forge
    libzlib-1.2.12             |       ha287fd2_1          48 KB  conda-forge
    openssl-1.1.1p             |       ha287fd2_0         1.8 MB  conda-forge
    zlib-1.2.12                |       ha287fd2_1          77 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         2.0 MB

The following packages will be UPDATED:

  ca-certificates                    2022.5.18.1-h4653dfc_0 --> 2022.6.15-h4653dfc_0
  libzlib                                 1.2.12-h90dfc92_0 --> 1.2.12-ha287fd2_1
  openssl                                 1.1.1o-ha287fd2_0 --> 1.1.1p-ha287fd2_0
  zlib                                    1.2.12-h90dfc92_0 --> 1.2.12-ha287fd2_1

I have accepted the update by entering y

Installed packages

# packages in environment at /opt/homebrew/Caskroom/miniforge/base:
#
# Name                    Version                   Build  Channel
brotlipy                  0.7.0           py39hb18efdd_1004    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
ca-certificates           2022.6.15            h4653dfc_0    conda-forge
certifi                   2022.5.18.1      py39h2804cbe_0    conda-forge
cffi                      1.15.0           py39h52b1de0_0    conda-forge
charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
conda                     4.12.0           py39h2804cbe_0    conda-forge
conda-package-handling    1.8.1            py39hb18efdd_1    conda-forge
cryptography              37.0.2           py39h4cb6239_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libzlib                   1.2.12               ha287fd2_1    conda-forge
ncurses                   6.3                  h07bb92c_1    conda-forge
openssl                   1.1.1p               ha287fd2_0    conda-forge
pip                       22.1.2             pyhd8ed1ab_0    conda-forge
pycosat                   0.6.3           py39hb18efdd_1010    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py39h2804cbe_5    conda-forge
python                    3.9.13          hc596b02_0_cpython    conda-forge
python_abi                3.9                      2_cp39    conda-forge
readline                  8.1                  hedafd6a_0    conda-forge
requests                  2.27.1             pyhd8ed1ab_0    conda-forge
ruamel_yaml               0.15.80         py39h9eb174b_1007    conda-forge
setuptools                62.3.2           py39h2804cbe_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.38.5               h40dfcc0_0    conda-forge
tk                        8.6.12               he1e0b03_0    conda-forge
tqdm                      4.64.0             pyhd8ed1ab_0    conda-forge
tzdata                    2022a                h191b570_0    conda-forge
urllib3                   1.26.9             pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xz                        5.2.5                h642e427_1    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
zlib                      1.2.12               ha287fd2_1    conda-forge

Environment info

active environment : None
            shell level : 0
       user config file : /Users/ningwang/.condarc
 populated config files : /opt/homebrew/Caskroom/miniforge/base/.condarc
                          /Users/ningwang/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.13.final.0
       virtual packages : __osx=12.4=0
                          __unix=0=0
                          __archspec=1=arm64
       base environment : /opt/homebrew/Caskroom/miniforge/base  (writable)
      conda av data dir : /opt/homebrew/Caskroom/miniforge/base/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /opt/homebrew/Caskroom/miniforge/base/pkgs
                          /Users/ningwang/.conda/pkgs
       envs directories : /opt/homebrew/Caskroom/miniforge/base/envs
                          /Users/ningwang/.conda/envs
               platform : osx-arm64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.13 Darwin/21.5.0 OSX/12.4
                UID:GID : 501:20
             netrc file : None
           offline mode : False
@nyngwang nyngwang added the bug Something isn't working label Jun 26, 2022
@nyngwang
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nyngwang commented Jun 26, 2022

I consider the:

The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:`

as no harm, so I have accepted the update. But still want to make a second check here.

@ustc-liu
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same problem here on my m1 mba.

@user799595
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Having the same issue unfortunately.

Completely clean install on Mambaforge (both arm64 and i386 on M1):

The following packages are causing the inconsistency:

  - conda-forge/noarch::requests==2.27.1=pyhd8ed1ab_0
  - conda-forge/osx-arm64::brotlipy==0.7.0=py39hb18efdd_1004
  - conda-forge/osx-arm64::setuptools==62.3.2=py39h2804cbe_0
  - conda-forge/noarch::six==1.16.0=pyh6c4a22f_0
  - conda-forge/noarch::charset-normalizer==2.0.12=pyhd8ed1ab_0
  - conda-forge/osx-arm64::python==3.9.13=hc596b02_0_cpython
  - conda-forge/osx-arm64::sqlite==3.38.5=h40dfcc0_0
  - conda-forge/osx-arm64::mamba==0.22.1=py39hde45b87_1
  - conda-forge/noarch::urllib3==1.26.9=pyhd8ed1ab_0
  - conda-forge/noarch::wheel==0.37.1=pyhd8ed1ab_0
  - conda-forge/osx-arm64::readline==8.1=hedafd6a_0
  - conda-forge/osx-arm64::ruamel_yaml==0.15.80=py39h9eb174b_1007
  - conda-forge/noarch::colorama==0.4.4=pyh9f0ad1d_0
  - conda-forge/osx-arm64::cffi==1.15.0=py39h52b1de0_0
  - conda-forge/noarch::pyopenssl==22.0.0=pyhd8ed1ab_0
  - conda-forge/noarch::tqdm==4.64.0=pyhd8ed1ab_0
  - conda-forge/noarch::pip==22.1.2=pyhd8ed1ab_0
  - conda-forge/noarch::idna==3.3=pyhd8ed1ab_0
  - conda-forge/osx-arm64::pysocks==1.7.1=py39h2804cbe_5
  - conda-forge/osx-arm64::pycosat==0.6.3=py39hb18efdd_1010
  - conda-forge/osx-arm64::cryptography==37.0.2=py39h4cb6239_0
  - conda-forge/osx-arm64::libmambapy==0.22.1=py39h43fb93c_1
  - conda-forge/osx-arm64::conda==4.12.0=py39h2804cbe_0
  - conda-forge/osx-arm64::python_abi==3.9=2_cp39
  - conda-forge/osx-arm64::conda-package-handling==1.8.1=py39hb18efdd_1
  - conda-forge/osx-arm64::certifi==2022.5.18.1=py39h2804cbe_0
  - conda-forge/noarch::pycparser==2.21=pyhd8ed1ab_0
done

Jupyter is also broken...

@mhdmyz
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mhdmyz commented Jul 7, 2022

Same problem here!

@hmaarrfk
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hmaarrfk commented Jul 7, 2022

Sorry for the delay. Ultimately, we aren't always able to recreate in every downstream packaged environment.

Can any of you recreate without homebrew? If not. You might get better help asking the homebrew devs directly :/

@user799595
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user799595 commented Jul 8, 2022

@hmaarrfk I don't think it's a homebrew issue, I used the installer https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-MacOSX-arm64.sh

As a workaround, I switched from Mambaforge to Miniconda

cd `mktemp -d`
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh
bash Miniconda3-latest-MacOSX-arm64.sh -b -p "$__conda_prefix"
echo "channels: [conda-forge]" > "$__conda_prefix/.condarc"
$__conda_prefix/bin/conda update -y --all
$__conda_prefix/bin/conda install -y mamba

This seems to work.

@hmaarrfk
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hmaarrfk commented Jul 8, 2022

Thank you for pointing me to that detail.

It is, indeed odd.

@hubzado
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hubzado commented Jul 10, 2022

Looks like it is fixed now. Updated all environments.

@mhdmyz
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mhdmyz commented Jul 10, 2022

Looks like it is fixed now. Updated all environments.

I doubt it! I still get the same errors!

@ustc-liu
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Looks like it is fixed now. Updated all environments.

I still got the same issue.

@jharrang
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There's a potential 1-line fix if using homebrew-installed mambaforge!

I seemingly was just able to fix this on a 2022 M1 MBP where I encountered this from a completely clean homebrew-installed mambaforge install by running (in the base environment):
mamba update --all

That updated conda to 4.13 and mamba to 0.24.0. It's possible that I'm no longer seeing the "inconsistent environment" warning by virtue of having no updateable packages, but at least for the time being this seems to have fixed things:

❯ conda update --all
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

@nyngwang
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~ % conda update -n base conda                                                                                                                                16:16:24
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

it seems that the problem is resolved now.

@ustc-liu
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```shell
~ % conda update -n base conda                                                                                                                                16:16:24
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

it seems that the problem is resolved now.

still got the errors

sheng@liu ~ % conda update -n base conda > 1.txt

The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  • conda-forge/noarch::requests==2.27.1=pyhd8ed1ab_0
  • conda-forge/osx-arm64::brotlipy==0.7.0=py39hb18efdd_1004
  • conda-forge/osx-arm64::setuptools==62.3.2=py39h2804cbe_0
  • conda-forge/noarch::six==1.16.0=pyh6c4a22f_0
  • conda-forge/noarch::charset-normalizer==2.0.12=pyhd8ed1ab_0
  • conda-forge/osx-arm64::python==3.9.13=hc596b02_0_cpython
  • conda-forge/osx-arm64::sqlite==3.38.5=h40dfcc0_0
  • conda-forge/noarch::urllib3==1.26.9=pyhd8ed1ab_0
  • conda-forge/noarch::wheel==0.37.1=pyhd8ed1ab_0
  • conda-forge/osx-arm64::readline==8.1=hedafd6a_0
  • conda-forge/osx-arm64::ruamel_yaml==0.15.80=py39h9eb174b_1007
  • conda-forge/noarch::colorama==0.4.4=pyh9f0ad1d_0
  • conda-forge/osx-arm64::cffi==1.15.0=py39h52b1de0_0
  • conda-forge/noarch::pyopenssl==22.0.0=pyhd8ed1ab_0
  • conda-forge/noarch::tqdm==4.64.0=pyhd8ed1ab_0
  • conda-forge/noarch::pip==22.1.2=pyhd8ed1ab_0
  • conda-forge/noarch::idna==3.3=pyhd8ed1ab_0
  • conda-forge/osx-arm64::pysocks==1.7.1=py39h2804cbe_5
  • conda-forge/osx-arm64::pycosat==0.6.3=py39hb18efdd_1010
  • conda-forge/osx-arm64::cryptography==37.0.2=py39h4cb6239_0
  • conda-forge/osx-arm64::conda==4.12.0=py39h2804cbe_0
  • conda-forge/osx-arm64::python_abi==3.9=2_cp39
  • conda-forge/osx-arm64::conda-package-handling==1.8.1=py39hb18efdd_1
  • conda-forge/osx-arm64::certifi==2022.5.18.1=py39h2804cbe_0
  • conda-forge/noarch::pycparser==2.21=pyhd8ed1ab_0

==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 4.13.0

Please update conda by running

$ conda update -n base conda

@bakj1979
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Brand new M1 MBP with freshly installed Miniforge and am getting the same errors.

Has a solution been found (either with AND without home-brew)?

The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  • conda-forge/noarch::requests==2.27.1=pyhd8ed1ab_0
  • conda-forge/osx-arm64::brotlipy==0.7.0=py39hb18efdd_1004
  • conda-forge/osx-arm64::setuptools==62.3.2=py39h2804cbe_0
  • conda-forge/noarch::six==1.16.0=pyh6c4a22f_0
  • conda-forge/noarch::charset-normalizer==2.0.12=pyhd8ed1ab_0
  • conda-forge/osx-arm64::python==3.9.13=hc596b02_0_cpython
  • conda-forge/osx-arm64::sqlite==3.38.5=h40dfcc0_0
  • conda-forge/noarch::urllib3==1.26.9=pyhd8ed1ab_0
  • conda-forge/noarch::wheel==0.37.1=pyhd8ed1ab_0
  • conda-forge/osx-arm64::readline==8.1=hedafd6a_0
  • conda-forge/osx-arm64::ruamel_yaml==0.15.80=py39h9eb174b_1007
  • conda-forge/noarch::colorama==0.4.4=pyh9f0ad1d_0
  • conda-forge/osx-arm64::cffi==1.15.0=py39h52b1de0_0
  • conda-forge/noarch::pyopenssl==22.0.0=pyhd8ed1ab_0
  • conda-forge/noarch::tqdm==4.64.0=pyhd8ed1ab_0
  • conda-forge/noarch::pip==22.1.2=pyhd8ed1ab_0
  • conda-forge/noarch::idna==3.3=pyhd8ed1ab_0
  • conda-forge/osx-arm64::pysocks==1.7.1=py39h2804cbe_5
  • conda-forge/osx-arm64::pycosat==0.6.3=py39hb18efdd_1010
  • conda-forge/osx-arm64::cryptography==37.0.2=py39h4cb6239_0
  • conda-forge/osx-arm64::conda==4.12.0=py39h2804cbe_0
  • conda-forge/osx-arm64::python_abi==3.9=2_cp39
  • conda-forge/osx-arm64::conda-package-handling==1.8.1=py39hb18efdd_1
  • conda-forge/osx-arm64::certifi==2022.5.18.1=py39h2804cbe_0
  • conda-forge/noarch::pycparser==2.21=pyhd8ed1ab_0
    done

==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 4.13.0

Please update conda by running

$ conda update -n base conda

@hmaarrfk
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@ngam are you able to help here? I don't have a mac, but it seems like you might have some useful input.

@ngam
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ngam commented Jul 17, 2022

I will try to reproduce...

@ngam
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ngam commented Jul 17, 2022

I can reproduce. When was the last time we updated our mambaforge/miniforge package list? Here are my quick thoughts ---

  1. This is an innocent warning in general, but if you are worried, just mamba update --all --yes and then mamba update -n base conda but if these two don't work, try the second point below:
  2. This seems like an issue deep in the weeds of some deps, it could be related to requests and charset-normalizer. Updating to the latest requests seems to resolve this mess, e.g. mamba update 'requests>=2.28.1'. Looking more closely though, the offending packages seem to be the most fundamental, ca-certificates, openssl, and readline, and updating these can also resolve this.

Full history of the second point:
We pushed a minor fix for requests recently and maybe this is relevant? Idk conda-forge/requests-feedstock#54. I do not believe we have updated any of our infrastructure to move beyond this. Hence, you still see the requests--chardet warnings in our CI and in most of our containers. This could be relevant.

TLDR

  • users: try mamba update --all and/or mamba install 'requests>=2.28.1'
  • maintainers: push new images (and installers) with updated packages especially requests and co

NOTE: mamba (not conda) in everything I said above; mamba update --all will fix everything, but conda update --all won't; however, conda install 'requests>=2.28.1' (which really only updates ca-certificates, openssl, and readline, so you could just update them individually instead) should fix things.

  ca-certificates                    2022.5.18.1-h4653dfc_0 --> 2022.6.15-h4653dfc_0
  openssl                                 1.1.1o-ha287fd2_0 --> 1.1.1q-ha287fd2_0
  readline                                   8.1-hedafd6a_0 --> 8.1.2-h46ed386_0

@ngam
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ngam commented Jul 17, 2022

@hmaarrfk I am not familiar how we decide to freeze a certain package list, but I am not sure why the default mambaforge is still stuck on an older conda/mamba combo. I think force-updating this (especially after the drama with mamba and conda breaking around the most recent updates) makes most sense. I am not too familiar with the logistics though, so idk if this idea makes any sense as a more sustainable solution.

/var/folders/1n/3mhwyfy56fsglfktknlw2c6m0000gn/T/tmp.z0qk6Dn0/.mambaforge/bin/mamba --version  
mamba 0.22.1
conda 4.12.0

@hmaarrfk
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Thanks for chiming in. I think there was some hesitancy in updating mamba though I think it has largely gone away.

Not sure why this PR has remained as a draft for so long.

#301

Hopefully next week we can move on it.

@ngam
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ngam commented Jul 17, 2022

Ah I see #301 now, though is it at all possible to just change the list of packages?

I tested the artifacts produced by #301 here https://github.com/conda-forge/miniforge/actions/runs/2660176511 and they don't have this issue on osx-arm64.

For a quick fix, could it be possible to just to rerun the actions without any changes (i.e. without bumping the version)?

@ngam
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ngam commented Jul 17, 2022

Fwiw, the latest PR's (pushed into main) artifacts in https://github.com/conda-forge/miniforge/actions/runs/2659924106 don't have this problem. So you could simply cut a release without even updating mamba version

@hmaarrfk
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We released a new version on miniforge. Hopefully it will get to homebrew soon and alleviate these problems

@ngam
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ngam commented Aug 3, 2022

@hmaarrfk this issue is now resolved. I tested it locally. Feel free to close it

@ngam
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ngam commented Aug 3, 2022

also: Homebrew/homebrew-cask#128931

@hmaarrfk
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hmaarrfk commented Aug 3, 2022

Thank you all for your patience. Feel free to open an issue if this comes up again. I think significant changes happened that it makes the information here somewhat stale

@hmaarrfk hmaarrfk closed this as completed Aug 3, 2022
@cstrlln
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cstrlln commented Aug 11, 2022

Hi, I installed miniforge a couple of weeks ago on and M1 and ran into the same issues described above.
As suggested tried doing a mambaforge install with brew but get this message:

Error: Cask 'mambaforge' conflicts with 'miniforge'.

Should I just try to reinstall everything?

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