Mamba does not include configured subdirs in package search

[jmeppley]

Using mamba to install bioconda packages on an M2 mac, I ran into the problem where packages only exist for the older intel architecture. The system can use those, but conda has to be configured to also look there with:

conda config --add subdirs osx-64

This works for conda, but mamba still does not find the packages.

(base) jmeppley@Johns-Air tmp % mamba create -p ./m.env minimap2

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

        mamba (0.25.0) supported by @QuantStack

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

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


Looking for: ['minimap2']

conda-forge/osx-arm64                                       Using cache
conda-forge/noarch                                          Using cache
bioconda/osx-arm64                                          Using cache
bioconda/noarch                                             Using cache
pkgs/main/noarch                                              No change
pkgs/r/noarch                                                 No change
pkgs/main/osx-arm64                                           No change
pkgs/r/osx-arm64                                              No change
Encountered problems while solving:
  - nothing provides requested minimap2

(base) jmeppley@Johns-Air tmp % conda create -p ./m.env minimap2 
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - minimap2

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


(base) jmeppley@Johns-Air tmp % conda search minimap2           
Loading channels: done
No match found for: minimap2. Search: *minimap2*

PackagesNotFoundError: The following packages are not available from current channels:

  - minimap2

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


(base) jmeppley@Johns-Air tmp % conda config --add subdirs osx-64
(base) jmeppley@Johns-Air tmp % mamba create -p ./m.env minimap2 

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

        mamba (0.25.0) supported by @QuantStack

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

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


Looking for: ['minimap2']

conda-forge/osx-arm64                                       Using cache
conda-forge/noarch                                          Using cache
bioconda/osx-arm64                                          Using cache
bioconda/noarch                                             Using cache
pkgs/main/osx-arm64                                           No change
pkgs/main/noarch                                              No change
pkgs/r/noarch                                                 No change
pkgs/r/osx-arm64                                              No change
Encountered problems while solving:
  - nothing provides requested minimap2

(base) jmeppley@Johns-Air tmp % conda create -p ./m.env minimap2
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/jmeppley/work/tmp/m.env

  added / updated specs:
    - minimap2


The following NEW packages will be INSTALLED:

  k8                 bioconda/osx-64::k8-0.2.5-h6151dfb_2
  libcxx             conda-forge/osx-64::libcxx-14.0.6-hce7ea42_0
  libzlib            conda-forge/osx-64::libzlib-1.2.12-hfe4f2af_2
  minimap2           bioconda/osx-64::minimap2-2.24-h1f540d2_1
  zlib               conda-forge/osx-64::zlib-1.2.12-hfe4f2af_2


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate /Users/jmeppley/work/tmp/m.env
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Retrieving notices: ...working... done