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The Fast Cross-Platform Package Manager
https://mamba.readthedocs.io
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Problem installing/finding packages #3261

Open pmomadeira opened 3 months ago

pmomadeira commented 3 months ago

Troubleshooting docs

Anaconda default channels

How did you install Mamba?

Micromamba

Search tried in issue tracker

critical libmamba Could not solve for environment specs

Latest version of Mamba

Tried in Conda?

I have this problem with Conda as well, without using Mamba

Describe your issue

Greetings,

The past few days/weeks I started having a lot of issues trying to install new libraries on my micromamba environments, or in conda environments. I try to install packages that I know exist in the repositories, using all the available options on anaconda's packages information, meaning I try to install them directly micromamba install package, with the channel information micromamba install bioconda::package, or even micromamba install biconda/label/cf201901::package.

Almost every package I've been trying to install is met with: error libmamba Could not solve for environment specs The following package could not be installed └─ package does not exist (perhaps a typo or a missing channel). critical libmamba Could not solve for environment specs

I've been looking around for possible solutions but I've been unable to find any. If anyone has met the same problem or has a solution I would greatly appreciate it.

Best regards

mamba info / micromamba info

libmamba version : 1.5.8
     micromamba version : 1.5.8
           curl version : libcurl/8.6.0 SecureTransport (OpenSSL/3.2.1) zlib/1.2.13 zstd/1.5.5 libssh2/1.11.0 nghttp2/1.58.0
     libarchive version : libarchive 3.7.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.5
       envs directories : /Users/pedromadeira/micromamba/envs
          package cache : /Users/pedromadeira/micromamba/pkgs
                          /Users/pedromadeira/.mamba/pkgs
            environment : EckEnv (active)
           env location : /Users/pedromadeira/micromamba/envs/EckEnv
      user config files : /Users/pedromadeira/.mambarc
 populated config files : /Users/pedromadeira/.mambarc
                          /Users/pedromadeira/.condarc
       virtual packages : __unix=0=0
                          __osx=14.3.1=0
                          __archspec=1=arm64
               channels : https://conda.anaconda.org/bioconda/osx-arm64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/nodefaults/osx-arm64
                          https://conda.anaconda.org/nodefaults/noarch
       base environment : /Users/pedromadeira/micromamba
               platform : osx-arm64

Logs

info     libmamba Parsing MatchSpec vcf-kit
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/bioconda/osx-arm64/repodata.json'
bioconda/osx-arm64                                          Using cache
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/bioconda/noarch/repodata.json'
bioconda/noarch                                             Using cache
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/conda-forge/osx-arm64/repodata.json'
conda-forge/osx-arm64                                       Using cache
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/conda-forge/noarch/repodata.json'
conda-forge/noarch                                          Using cache
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/nodefaults/osx-arm64/repodata.json'
info     libmamba No valid cache found
info     libmamba Expired cache (or invalid mod/etag headers) found at '/Users/pedromadeira/micromamba/pkgs'
info     libmamba Using macOS SecureTransport backend
info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/nodefaults/noarch/repodata.json'
info     libmamba No valid cache found
info     libmamba Expired cache (or invalid mod/etag headers) found at '/Users/pedromadeira/micromamba/pkgs'
info     libmamba All targets to download are cached
info     libmamba Starting to download targets
[+] 0.3s
nodefaults/osx-arm64 ━━━━━╸━━━━━━━━━━━━━━━╸━━   0.0 B /  ??.?MB @  ??.?MB/s  0.3s
nodefaults/noarch    ━━━━━━━━━━━╸━━━━━━━━━━━━   0.0 B /  ??.?MB @  ??.?MB/s  0.3sinfo     libmamba Transfer done for 'nodefaults/noarch'
info     libmamba Transfer finalized, status: 304 [https://conda.anaconda.org/nodefaults/noarch/repodata.json.zst] 0 bytes
info     libmamba Cache is still valid
info     libmamba Transfer done for 'nodefaults/osx-arm64'
info     libmamba Transfer finalized, status: 304 [https://conda.anaconda.org/nodnodefaults/noarch                                             No change
nodefaults/osx-arm64                                          No change
info     libmamba Reading cache files '/Users/pedromadeira/micromamba/pkgs/cache/57e79ec4.solv.*' for repo index 'bioconda/osx-arm64'
info     libmamba Attempting to read libsolv solv file "/Users/pedromadeira/micromamba/pkgs/cache/57e79ec4.solv" for repo bioconda/osx-arm64
info     libmamba Expecting solv metadata : {"etag":"W/\"bd18071599942dd824e1ec40e9d10873\"","mod":"Wed, 04 May 2022 16:25:08 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/bioconda/osx-arm64"}
info     libmamba Loaded solv metadata : {"etag":"W/\"bd18071599942dd824e1ec40e9d10873\"","mod":"Wed, 04 May 2022 16:25:08 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/bioconda/osx-arm64"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Reading cache files '/Users/pedromadeira/micromamba/pkgs/cache/2a957770.solv.*' for repo index 'bioconda/noarch'
info     libmamba Attempting to read libsolv solv file "/Users/pedromadeira/micromamba/pkgs/cache/2a957770.solv" for repo bioconda/noarch
info     libmamba Expecting solv metadata : {"etag":"W/\"ce096913f0008099e5cf31370dc2d0ce-5\"","mod":"Mon, 01 Apr 2024 19:11:15 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/bioconda/noarch"}
info     libmamba Loaded solv metadata : {"etag":"W/\"ce096913f0008099e5cf31370dc2d0ce-5\"","mod":"Mon, 01 Apr 2024 19:11:15 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/bioconda/noarch"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Reading cache files '/Users/pedromadeira/micromamba/pkgs/cache/a850f475.solv.*' for repo index 'conda-forge/osx-arm64'
info     libmamba Attempting to read libsolv solv file "/Users/pedromadeira/micromamba/pkgs/cache/a850f475.solv" for repo conda-forge/osx-arm64
info     libmamba Expecting solv metadata : {"etag":"\"04a47f6caf3d5b9788855469a99ee554\"","mod":"Mon, 01 Apr 2024 22:50:51 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/conda-forge/osx-arm64"}
info     libmamba Loaded solv metadata : {"etag":"\"04a47f6caf3d5b9788855469a99ee554\"","mod":"Mon, 01 Apr 2024 22:50:51 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/conda-forge/osx-arm64"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Reading cache files '/Users/pedromadeira/micromamba/pkgs/cache/09cdf8bf.solv.*' for repo index 'conda-forge/noarch'
info     libmamba Attempting to read libsolv solv file "/Users/pedromadeira/micromamba/pkgs/cache/09cdf8bf.solv" for repo conda-forge/noarch
info     libmamba Expecting solv metadata : {"etag":"\"7c727fee0e6a79d8aadce8507296a91b\"","mod":"Mon, 01 Apr 2024 20:00:34 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/conda-forge/noarch"}
info     libmamba Loaded solv metadata : {"etag":"\"7c727fee0e6a79d8aadce8507296a91b\"","mod":"Mon, 01 Apr 2024 20:00:34 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/conda-forge/noarch"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Reading cache files '/Users/pedromadeira/micromamba/pkgs/cache/ef10d206.solv.*' for repo index 'nodefaults/osx-arm64'
info     libmamba Attempting to read libsolv solv file "/Users/pedromadeira/micromamba/pkgs/cache/ef10d206.solv" for repo nodefaults/osx-arm64
info     libmamba Expecting solv metadata : {"etag":"","mod":"Wed, 24 Aug 2016 16:31:12 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/nodefaults/osx-arm64"}
info     libmamba Loaded solv metadata : {"etag":"","mod":"Wed, 24 Aug 2016 16:31:12 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/nodefaults/osx-arm64"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Reading cache files '/Users/pedromadeira/micromamba/pkgs/cache/223a346e.solv.*' for repo index 'nodefaults/noarch'
info     libmamba Attempting to read libsolv solv file "/Users/pedromadeira/micromamba/pkgs/cache/223a346e.solv" for repo nodefaults/noarch
info     libmamba Expecting solv metadata : {"etag":"","mod":"Wed, 24 Aug 2016 16:31:12 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/nodefaults/noarch"}
info     libmamba Loaded solv metadata : {"etag":"","mod":"Wed, 24 Aug 2016 16:31:12 GMT","pip_added":true,"tool_version":"1.3_0.7.28","url":"https://conda.anaconda.org/nodefaults/noarch"}
info     libmamba Metadata from solv are valid, loading successful
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libzlib-1.2.13-h53f4e23_5.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/six-1.16.0-pyh6c4a22f_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/numpy-1.26.4-py312h8442bc7_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/python-3.12.2-hdf0ec26_0_cpython.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libexpat-2.6.2-hebf3989_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/markupsafe-2.1.5-py312he37b823_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/typing_extensions-4.10.0-pyha770c72_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/xz-5.2.6-h57fd34a_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/fsspec-2024.3.1-pyhca7485f_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libtorch-2.1.2-cpu_generic_hff38252_3.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/pyvcf3-1.0.3-pyhdfd78af_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/networkx-3.2.1-pyhd8ed1ab_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/mpmath-1.3.0-pyhd8ed1ab_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/sympy-1.12-pyh04b8f61_3.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libprotobuf-4.25.1-h810fc01_2.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/jinja2-3.1.3-pyhd8ed1ab_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/scipy-1.12.0-py312h9d7df2b_2.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/readline-8.2-h92ec313_1.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/pytorch-2.1.2-cpu_generic_py312hb841a54_3.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libffi-3.4.2-h3422bc3_5.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/python-tzdata-2024.1-pyhd8ed1ab_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/tk-8.6.13-h5083fa2_1.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/pandas-2.2.1-py312h88edd18_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libcblas-3.9.0-21_osxarm64_openblas.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/python-dateutil-2.9.0-pyhd8ed1ab_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libabseil-20230802.1-cxx17_h13dd4ca_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/pytz-2024.1-pyhd8ed1ab_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/liblapack-3.9.0-21_osxarm64_openblas.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libsqlite-3.45.2-h091b4b1_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libgfortran-5.0.0-13_2_0_hd922786_3.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/openssl-3.2.1-h0d3ecfb_1.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/filelock-3.13.3-pyhd8ed1ab_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/pip-24.0-pyhd8ed1ab_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libopenblas-0.3.26-openmp_h6c19121_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/setuptools-69.2.0-pyhd8ed1ab_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/ncurses-6.4.20240210-h078ce10_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libuv-1.48.0-h93a5062_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/bzip2-1.0.8-h93a5062_5.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libcxx-16.0.6-h4653b0c_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/nomkl-1.0-h5ca1d4c_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libblas-3.9.0-21_osxarm64_openblas.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/tzdata-2024a-h0c530f3_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/python_abi-3.12-4_cp312.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/ca-certificates-2024.2.2-hf0a4a13_0.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/libgfortran5-13.2.0-hf226fd6_3.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/wheel-0.43.0-pyhd8ed1ab_1.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/sleef-3.5.1-h156473d_2.json"
info     libmamba Loading single package record: "/Users/pedromadeira/micromamba/envs/EckEnv/conda-meta/llvm-openmp-18.1.2-hcd81f8e_0.json"
info     libmamba Adding package record to repo __archspec
info     libmamba Adding package record to repo __osx
info     libmamba Adding package record to repo __unix
info     libmamba Adding package record to repo bzip2
info     libmamba Adding package record to repo ca-certificates
info     libmamba Adding package record to repo filelock
info     libmamba Adding package record to repo fsspec
info     libmamba Adding package record to repo jinja2
info     libmamba Adding package record to repo libabseil
info     libmamba Adding package record to repo libblas
info     libmamba Adding package record to repo libcblas
info     libmamba Adding package record to repo libcxx
info     libmamba Adding package record to repo libexpat
info     libmamba Adding package record to repo libffi
info     libmamba Adding package record to repo libgfortran
info     libmamba Adding package record to repo libgfortran5
info     libmamba Adding package record to repo liblapack
info     libmamba Adding package record to repo libopenblas
info     libmamba Adding package record to repo libprotobuf
info     libmamba Adding package record to repo libsqlite
info     libmamba Adding package record to repo libtorch
info     libmamba Adding package record to repo libuv
info     libmamba Adding package record to repo libzlib
info     libmamba Adding package record to repo llvm-openmp
info     libmamba Adding package record to repo markupsafe
info     libmamba Adding package record to repo mpmath
info     libmamba Adding package record to repo ncurses
info     libmamba Adding package record to repo networkx
info     libmamba Adding package record to repo nomkl
info     libmamba Adding package record to repo numpy
info     libmamba Adding package record to repo openssl
info     libmamba Adding package record to repo pandas
info     libmamba Adding package record to repo pip
info     libmamba Adding package record to repo python
info     libmamba Adding package record to repo python-dateutil
info     libmamba Adding package record to repo python-tzdata
info     libmamba Adding package record to repo python_abi
info     libmamba Adding package record to repo pytorch
info     libmamba Adding package record to repo pytz
info     libmamba Adding package record to repo pyvcf3
info     libmamba Adding package record to repo readline
info     libmamba Adding package record to repo scipy
info     libmamba Adding package record to repo setuptools
info     libmamba Adding package record to repo six
info     libmamba Adding package record to repo sleef
info     libmamba Adding package record to repo sympy
info     libmamba Adding package record to repo tk
info     libmamba Adding package record to repo typing_extensions
info     libmamba Adding package record to repo tzdata
info     libmamba Adding package record to repo wheel
info     libmamba Adding package record to repo xz
info     libmamba Parsing MatchSpec vcf-kit
info     libmamba Parsing MatchSpec python 3.12.*
info     libmamba Parsing MatchSpec pin-1
info     libmamba Adding job: pin-1
info     libmamba Parsing MatchSpec pin-1
info     libmamba Parsing MatchSpec pin-1
info     libmamba Adding job: pin-1

Pinned packages:
  - python 3.12.*

info     libmamba Parsing MatchSpec vcf-kit
info     libmamba Parsing MatchSpec vcf-kit
info     libmamba Adding job: vcf-kit
info     libmamba Problem count: 1
info     libmamba Parsing MatchSpec vcf-kit
info     libmamba Parsing MatchSpec vcf-kit
error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ vcf-kit does not exist (perhaps a typo or a missing channel).
critical libmamba Could not solve for environment specs

environment.yml

name: EckEnv
channels:
- bioconda
- conda-forge
dependencies:
- pandas
- bioconda::pyvcf3
- scipy

~/.condarc

changeps1: false

EDIT: Hi again, I just wanted to add some more information to this problem. I have tested conda and micromamba in a linux machine with an older version of both conda and micromamba (and libmamba) and the problem does not replicate. I have tried downgrading both on my masOS M1 and the problem still subsists, so I really don't know what else to do