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The Fast Cross-Platform Package Manager
https://mamba.readthedocs.io
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`micromamba update --all` pretends to but doesn't actually update a `mamba` activated/owned environment #3569

Closed corneliusroemer closed 4 days ago

corneliusroemer commented 1 month ago

Troubleshooting docs

Anaconda default channels

How did you install Mamba?

Micromamba

Search tried in issue tracker

update --all

Latest version of Mamba

Tried in Conda?

I do not have this problem with Conda, just with Mamba

Describe your issue

TLDR: When I activate a mamba (not micromamba!) environment and run micromamba update --all -y --platform osx-arm64, micromamba pretends to update the activated environment but doesn't actually.

Longer story: I have a really weird setup, but maybe it does uncover some unintended behaviour more generally. As part of a general system update procedure I run daily, I activate and update all sorts of conda/mamba/micromamba environments.

Recently, something weird started to happen without having done any changes to the commands invoked: micromamba seemed to perform the same update every time I ran the update command - but it didn't actually change anything. What I'm doing is definitely somewhat weird, but micromamba is still behaving unexpectedly so bear with me.

The interesting thing here seems to be that mamba activate py11 works, but micromamba activate py11 doesn't work, yet the mamba activate affects micromamba commands later on:

❯ micromamba activate py11
critical libmamba Cannot activate, prefix does not exist at: '/Users/corneliusromer/micromamba/envs/py11'

Maybe this makes it reproducible:

  1. Install mamba v2.0.2 and micromamba v2.0.2
  2. Add the wrappers to the shell init: 
    
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/homebrew/Caskroom/miniforge/base/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/opt/homebrew/Caskroom/miniforge/base/etc/profile.d/conda.sh" ]; then
    . "/opt/homebrew/Caskroom/miniforge/base/etc/profile.d/conda.sh"
else
    export PATH="/opt/homebrew/Caskroom/miniforge/base/bin:$PATH"
fi
fi
unset __conda_setup

if [ -f "/opt/homebrew/Caskroom/miniforge/base/etc/profile.d/mamba.sh" ]; then . "/opt/homebrew/Caskroom/miniforge/base/etc/profile.d/mamba.sh" fi

<<< conda initialize <<<

>>> mamba initialize >>>

!! Contents within this block are managed by 'micromamba shell init' !!

export MAMBA_EXE='/Users/corneliusromer/.local/bin/micromamba'; export MAMBA_ROOT_PREFIX='/Users/corneliusromer/micromamba'; mamba_setup="$("$MAMBA_EXE" shell hook --shell zsh --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)" if [ $? -eq 0 ]; then eval "$mamba_setup" else alias micromamba="$MAMBA_EXE" # Fallback on help from micromamba activate fi unset __mamba_setup

<<< mamba initialize <<<

3. Create an environment `py11` with yaml see below
4. Run `mamba activate py11`
5. Run `micromamba update --all -y --platform osx-arm64 --log-level 4`
6. Run `mamba deactivate`
7. Rinse repeat, observe that the same changes are done every time, suggesting the update _isn't_ actually going through

### mamba info / micromamba info

```shell
$ mamba info

       libmamba version : 2.0.2
     micromamba version : 2.0.2
           curl version : libcurl/8.9.1 (OpenSSL/3.3.2) SecureTransport zlib/1.3.1 zstd/1.5.6 libssh2/1.11.0 nghttp2/1.58.0
     libarchive version : libarchive 3.7.4 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.6
       envs directories : /Users/corneliusromer/micromamba/envs
          package cache : /Users/corneliusromer/micromamba/pkgs
                          /Users/corneliusromer/.mamba/pkgs
            environment : /opt/homebrew/Caskroom/miniforge/base/envs/py11 (active)
           env location : /opt/homebrew/Caskroom/miniforge/base/envs/py11
      user config files : /Users/corneliusromer/.mambarc
 populated config files : /Users/corneliusromer/.mambarc
                          /Users/corneliusromer/.condarc
       virtual packages : __unix=0=0
                          __osx=15.0.1=0
                          __archspec=1=arm64
               channels : https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/bioconda/osx-arm64
                          https://conda.anaconda.org/nodefaults/noarch
                          https://conda.anaconda.org/nodefaults/osx-arm64
       base environment : /Users/corneliusromer/micromamba
               platform : osx-arm64

$ micromamba info

       libmamba version : 2.0.2
     micromamba version : 2.0.2
           curl version : libcurl/8.9.1 (OpenSSL/3.3.2) SecureTransport zlib/1.3.1 zstd/1.5.6 libssh2/1.11.0 nghttp2/1.58.0
     libarchive version : libarchive 3.7.4 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.6
       envs directories : /Users/corneliusromer/micromamba/envs
          package cache : /Users/corneliusromer/micromamba/pkgs
                          /Users/corneliusromer/.mamba/pkgs
            environment : /opt/homebrew/Caskroom/miniforge/base/envs/py11 (active)
           env location : /opt/homebrew/Caskroom/miniforge/base/envs/py11
      user config files : /Users/corneliusromer/.mambarc
 populated config files : /Users/corneliusromer/.mambarc
                          /Users/corneliusromer/.condarc
       virtual packages : __unix=0=0
                          __osx=15.0.1=0
                          __archspec=1=arm64
               channels : https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/bioconda/osx-arm64
                          https://conda.anaconda.org/nodefaults/noarch
                          https://conda.anaconda.org/nodefaults/osx-arm64
       base environment : /Users/corneliusromer/micromamba
               platform : osx-arm64

Logs

$ micromamba update --all -y --platform osx-arm64
conda-forge/noarch                                          Using cache
conda-forge/osx-arm64                                       Using cache
bioconda/noarch                                             Using cache
bioconda/osx-arm64                                          Using cache

Pinned packages:

  - pandas=1

Pinned packages:

  - numpy=1

Pinned packages:

  - pyarrow=15

Pinned packages:

  - snakemake!=7.29.0

Pinned packages:

  - jsonschema=3

Pinned packages:

  - typer[version="!=0.12.0,(!=0.12.1,(!=0.12.2,!=0.12.3))"]

Pinned packages:

  - python=3.11

Transaction

  Prefix: /opt/homebrew/Caskroom/miniforge/base/envs/py11

  No specs added or removed.

  Package                  Version  Build               Channel           Size
────────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────────

  + cpp-expected             1.1.0  hffc8910_0          conda-forge     Cached
  + nlohmann_json           3.11.3  h00cdb27_1          conda-forge     Cached
  + ruamel_yaml            0.15.80  py311heffc1b2_1009  conda-forge     Cached
  + simdjson                3.10.1  h7b3277c_0          conda-forge     Cached

  Remove:
────────────────────────────────────────────────────────────────────────────────

  - archspec                 0.2.3  pyhd8ed1ab_0        conda-forge     Cached
  - conda-libmamba-solver   24.9.0  pyhd8ed1ab_0        conda-forge     Cached
  - frozendict               2.4.6  py311hae2e1ce_0     conda-forge     Cached
  - menuinst                 2.1.2  py311h267d04e_1     conda-forge     Cached
  - truststore              0.10.0  pyhd8ed1ab_0        conda-forge     Cached

  Upgrade:
────────────────────────────────────────────────────────────────────────────────

  - libmamba                1.5.10  h66a2e1b_1          conda-forge     Cached
  + libmamba                 2.0.2  hc61166f_1          conda-forge     Cached
  - libmambapy              1.5.10  py311h2e2787a_1     conda-forge     Cached
  + libmambapy               2.0.2  py311hb3c77e8_1     conda-forge     Cached
  - mamba                   1.5.10  py311hb045da1_1     conda-forge     Cached
  + mamba                    2.0.2  h232bcfd_1          conda-forge     Cached

  Downgrade:
────────────────────────────────────────────────────────────────────────────────

  - conda                   24.9.2  py311h267d04e_0     conda-forge     Cached
  + conda                   22.9.0  py311h267d04e_2     conda-forge     Cached

  Summary:

  Install: 4 packages
  Remove: 5 packages
  Upgrade: 3 packages
  Downgrade: 1 packages

  Total download: 0 B

────────────────────────────────────────────────────────────────────────────────

Transaction starting
Unlinking archspec-0.2.3-pyhd8ed1ab_0
Unlinking conda-libmamba-solver-24.9.0-pyhd8ed1ab_0
Unlinking frozendict-2.4.6-py311hae2e1ce_0
Unlinking menuinst-2.1.2-py311h267d04e_1
Unlinking truststore-0.10.0-pyhd8ed1ab_0
Unlinking conda-24.9.2-py311h267d04e_0
Unlinking libmamba-1.5.10-h66a2e1b_1
Unlinking mamba-1.5.10-py311hb045da1_1
Unlinking libmambapy-1.5.10-py311h2e2787a_1
Linking cpp-expected-1.1.0-hffc8910_0
Linking simdjson-3.10.1-h7b3277c_0
Linking ruamel_yaml-0.15.80-py311heffc1b2_1009
Linking nlohmann_json-3.11.3-h00cdb27_1
Linking conda-22.9.0-py311h267d04e_2
Linking libmamba-2.0.2-hc61166f_1
Linking mamba-2.0.2-h232bcfd_1
Linking libmambapy-2.0.2-py311hb3c77e8_1

Transaction finished

environment.yml

name: py11
channels:
- bioconda
- conda-forge
- pkgs/main
dependencies:
- aioeasywebdav=2.4.0=pyha770c72_0
- aiohappyeyeballs=2.4.3=pyhd8ed1ab_0
- aiohttp=3.10.10=py311h0ecf0c1_0
- aiosignal=1.3.1=pyhd8ed1ab_0
- amply=0.1.6=pyhd8ed1ab_0
- annotated-types=0.7.0=pyhd8ed1ab_0
- anyio=4.6.2.post1=pyhd8ed1ab_0
- appdirs=1.4.4=pyh9f0ad1d_0
- appnope=0.1.4=pyhd8ed1ab_0
- archspec=0.2.3=pyhd8ed1ab_0
- argcomplete=3.5.1=pyhd8ed1ab_0
- argparse-dataclass=2.0.0=pyhd8ed1ab_0
- asciigenome=1.18.0=hdfd78af_0
- asttokens=2.4.1=pyhd8ed1ab_0
- async-timeout=4.0.3=pyhd8ed1ab_0
- attmap=0.13.2=pyhd8ed1ab_0
- attrs=24.2.0=pyh71513ae_0
- autoflake=1.7.5=pyhd8ed1ab_0
- autopep8=2.3.1=pyhd8ed1ab_0
- aws-c-auth=0.7.31=hee1f4ab_5
- aws-c-cal=0.7.4=hfd083d3_4
- aws-c-common=0.9.31=h7ab814d_0
- aws-c-compression=0.2.19=hfd083d3_4
- aws-c-event-stream=0.5.0=h33c80d7_0
- aws-c-http=0.8.10=h4a91a90_5
- aws-c-io=0.14.20=h5fdde16_2
- aws-c-mqtt=0.10.7=hd821a15_5
- aws-c-s3=0.7.0=hc6bcb7c_0
- aws-c-sdkutils=0.1.19=hfd083d3_6
- aws-checksums=0.1.20=hfd083d3_3
- aws-crt-cpp=0.29.0=h45f4ed5_0
- aws-sdk-cpp=1.11.407=h0a0d3c4_6
- azure-core-cpp=1.14.0=hd50102c_0
- azure-identity-cpp=1.10.0=hc602bab_0
- azure-storage-blobs-cpp=12.13.0=h7585a09_1
- azure-storage-common-cpp=12.8.0=h9ca1f76_1
- azure-storage-files-datalake-cpp=12.12.0=hcdd55da_1
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=pyhd8ed1ab_4
- backports.cached-property=1.0.2=pyhd8ed1ab_0
- backports.functools_lru_cache=2.0.0=pyhd8ed1ab_0
- backports.zoneinfo=0.2.1=py311h267d04e_9
- bcrypt=4.2.0=py311h481aa64_1
- beautifulsoup4=4.12.3=pyha770c72_0
- biopython=1.84=py311hd3f4193_0
- black=24.10.0=py311h267d04e_0
- bleach=6.1.0=pyhd8ed1ab_0
- blinker=1.8.2=pyhd8ed1ab_0
- blosc=1.21.6=h5499902_0
- boltons=24.0.0=pyhd8ed1ab_0
- boost-cpp=1.85.0=h103c1d6_4
- boto3=1.35.50=pyhd8ed1ab_0
- botocore=1.35.50=pyge310_1234567_0
- bottle=0.12.23=pyhd8ed1ab_0
- branca=0.7.2=pyhd8ed1ab_0
- brotli=1.1.0=hd74edd7_2
- brotli-bin=1.1.0=hd74edd7_2
- brotli-python=1.1.0=py311h3f08180_2
- brotlipy=0.7.0=py311h460d6c5_1007
- bz2file=0.98=py_0
- bzip2=1.0.8=h99b78c6_7
- c-ares=1.34.2=h7ab814d_0
- ca-certificates=2024.8.30=hf0a4a13_0
- cachecontrol=0.14.0=pyhd8ed1ab_1
- cachecontrol-with-filecache=0.14.0=pyhd8ed1ab_1
- cachetools=5.5.0=pyhd8ed1ab_0
- certifi=2024.8.30=pyhd8ed1ab_0
- cffi=1.17.1=py311h3a79f62_0
- cfitsio=4.4.1=hd313823_2
- chardet=5.2.0=py311h267d04e_2
- charset-normalizer=3.4.0=pyhd8ed1ab_0
- clang=19.1.2=default_h89fcaf4_1
- clang-19=19.1.2=default_h01e2e8e_1
- cleo=2.1.0=pyhd8ed1ab_0
- click=8.1.7=unix_pyh707e725_0
- click-default-group=1.2.4=pyhd8ed1ab_0
- click-plugins=1.1.1=py_0
- cligj=0.7.2=pyhd8ed1ab_1
- coin-or-cbc=2.10.12=h7cfbe6c_1
- coin-or-cgl=0.60.9=hbf821b3_0
- coin-or-clp=1.17.10=hde4c74c_0
- coin-or-osi=0.108.11=hfbf3c2f_1
- coin-or-utils=2.11.12=h1ec7d49_1
- coincbc=2.10.12=1_metapackage
- colorama=0.4.6=pyhd8ed1ab_0
- comm=0.2.2=pyhd8ed1ab_0
- commonmark=0.9.1=py_0
- conan=2.8.1=pyhd8ed1ab_0
- conda=24.9.2=py311h267d04e_0
- conda-inject=1.3.2=pyhd8ed1ab_0
- conda-libmamba-solver=24.9.0=pyhd8ed1ab_0
- conda-package-handling=2.4.0=pyh7900ff3_0
- conda-package-streaming=0.11.0=pyhd8ed1ab_0
- configargparse=1.7=pyhd8ed1ab_0
- connection_pool=0.0.3=pyhd3deb0d_0
- contourpy=1.3.0=py311h2c37856_2
- country_converter=1.2=pyhd8ed1ab_0
- cram=0.7=pyhd3eb1b0_1
- crashtest=0.4.1=pyhd8ed1ab_0
- cryptography=43.0.3=py311h544b224_0
- curl=8.10.1=h13a7ad3_0
- cycler=0.12.1=pyhd8ed1ab_0
- cyrus-sasl=2.1.27=h60b93bd_7
- dataclasses=0.8=pyhc8e2a94_3
- datrie=0.8.2=py311h460d6c5_8
- debugpy=1.8.7=py311h3f08180_0
- decorator=5.1.1=pyhd8ed1ab_0
- defusedxml=0.7.1=pyhd8ed1ab_0
- distlib=0.3.9=pyhd8ed1ab_0
- distro=1.8.0=pyhd8ed1ab_0
- docformatter=1.7.5=pyhd8ed1ab_0
- docutils=0.21.2=pyhd8ed1ab_0
- dpath=2.2.0=pyha770c72_0
- dropbox=11.36.2=pyhd8ed1ab_0
- dulwich=0.21.7=py311hae2e1ce_1
- eido=0.2.4=pyhd8ed1ab_0
- entrypoints=0.4=pyhd8ed1ab_0
- et_xmlfile=2.0.0=pyhd8ed1ab_0
- exceptiongroup=1.2.2=pyhd8ed1ab_0
- executing=2.1.0=pyhd8ed1ab_0
- expat=2.6.3=hf9b8971_0
- fasteners=0.17.3=pyhd8ed1ab_0
- fftw=3.3.10=nompi_h6637ab6_110
- filechunkio=1.8=py_2
- filelock=3.16.1=pyhd8ed1ab_0
- flask=3.0.3=pyhd8ed1ab_0
- flask_cors=4.0.0=pyhd8ed1ab_0
- fmt=11.0.2=h420ef59_0
- folium=0.18.0=pyhd8ed1ab_0
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=h77eed37_3
- fontconfig=2.14.2=h82840c6_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.54.1=py311h56c23cb_1
- freetype=2.12.1=hadb7bae_2
- freexl=2.0.0=hfbad9fb_0
- fribidi=1.0.10=h27ca646_0
- frozendict=2.4.6=py311hae2e1ce_0
- frozenlist=1.5.0=py311hae2e1ce_0
- ftputil=5.1.0=pyhd8ed1ab_0
- future=1.0.0=pyhd8ed1ab_0
- geographiclib=2.0=pyhd8ed1ab_0
- geopandas-base=1.0.1=pyha770c72_1
- geopy=2.4.1=pyhd8ed1ab_1
- geos=3.13.0=hf9b8971_0
- geotiff=1.7.3=h82bf549_3
- gflags=2.2.2=hf9b8971_1005
- ghostscript=10.04.0=hf9b8971_0
- giflib=5.2.2=h93a5062_0
- gitdb=4.0.11=pyhd8ed1ab_0
- gitpython=3.1.43=pyhd8ed1ab_0
- glog=0.7.1=heb240a5_0
- google-crc32c=1.1.2=py311hec9401f_6
- google-resumable-media=2.7.2=pyhd8ed1ab_1
- googleapis-common-protos=1.65.0=pyhd8ed1ab_0
- graphite2=1.3.13=hebf3989_1003
- grpcio=1.65.5=py311hc367efa_0
- h11=0.14.0=pyhd8ed1ab_0
- h2=4.1.0=pyhd8ed1ab_0
- hdf4=4.2.15=h2ee6834_7
- hdf5=1.14.3=nompi_hec07895_105
- hpack=4.0.0=pyh9f0ad1d_0
- html5lib=1.1=pyhd8ed1ab_1
- httpcore=1.0.6=pyhd8ed1ab_0
- httplib2=0.22.0=pyhd8ed1ab_0
- httpx=0.27.2=pyhd8ed1ab_0
- humanfriendly=10.0=pyhd8ed1ab_6
- hyperframe=6.0.1=pyhd8ed1ab_0
- hypothesis=6.115.5=pyha770c72_0
- icu=75.1=hfee45f7_0
- idna=3.10=pyhd8ed1ab_0
- immutables=0.21=py311h460d6c5_0
- importlib-metadata=8.5.0=pyha770c72_0
- importlib_metadata=8.5.0=hd8ed1ab_0
- importlib_resources=6.4.5=pyhd8ed1ab_0
- iniconfig=2.0.0=pyhd8ed1ab_0
- ipdb=0.13.13=pyhd8ed1ab_0
- ipykernel=6.29.5=pyh57ce528_0
- ipython=8.29.0=pyh707e725_0
- isort=5.13.2=pyhd8ed1ab_0
- itsdangerous=2.2.0=pyhd8ed1ab_0
- jaraco.classes=3.4.0=pyhd8ed1ab_1
- jbig=2.1=h3422bc3_2003
- jedi=0.19.1=pyhd8ed1ab_0
- jinja2=3.1.4=pyhd8ed1ab_0
- jiter=0.6.1=py311h481aa64_0
- jmespath=1.0.1=pyhd8ed1ab_0
- joblib=1.4.2=pyhd8ed1ab_0
- json-c=0.18=he4178ee_0
- jsonpatch=1.33=pyhd8ed1ab_0
- jsonpointer=3.0.0=py311h267d04e_1
- jsonschema=3.2.0=pyhd8ed1ab_3
- jsonschema-specifications=2024.10.1=pyhd8ed1ab_0
- jupyter_client=8.6.3=pyhd8ed1ab_0
- jupyter_core=5.7.2=pyh31011fe_1
- jupyterlab_pygments=0.3.0=pyhd8ed1ab_1
- kealib=1.5.3=h8edbb62_2
- keyring=24.3.1=pyh534df25_1
- kiwisolver=1.4.7=py311h2c37856_0
- krb5=1.21.3=h237132a_0
- lcms2=2.16=ha0e7c42_0
- lerc=4.0.0=h9a09cb3_0
- libabseil=20240722.0=cxx17_hf9b8971_1
- libaec=1.1.3=hebf3989_0
- libarchive=3.7.4=h83d404f_0
- libblas=3.9.0=25_osxarm64_openblas
- libboost=1.85.0=hf763ba5_4
- libboost-devel=1.85.0=hf450f58_4
- libboost-headers=1.85.0=hce30654_4
- libbrotlicommon=1.1.0=hd74edd7_2
- libbrotlidec=1.1.0=hd74edd7_2
- libbrotlienc=1.1.0=hd74edd7_2
- libcblas=3.9.0=25_osxarm64_openblas
- libclang-cpp19.1=19.1.2=default_h01e2e8e_1
- libcrc32c=1.1.2=hbdafb3b_0
- libcurl=8.10.1=h13a7ad3_0
- libcxx=19.1.2=ha82da77_0
- libdeflate=1.22=hd74edd7_0
- libedit=3.1.20191231=hc8eb9b7_2
- libev=4.33=h93a5062_2
- libevent=2.1.12=h2757513_1
- libexpat=2.6.3=hf9b8971_0
- libffi=3.4.2=h3422bc3_5
- libgd=2.3.3=hac1b3a8_10
- libgfortran=5.0.0=13_2_0_hd922786_3
- libgfortran5=13.2.0=hf226fd6_3
- libgoogle-cloud=2.30.0=h2e6cea1_0
- libgoogle-cloud-storage=2.30.0=h90fd6fa_0
- libgrpc=1.65.5=h3d9cf25_0
- libiconv=1.17=h0d3ecfb_2
- libint=2.9.0=hb2e4e21_2
- libintl=0.22.5=h8414b35_3
- libjpeg-turbo=3.0.0=hb547adb_1
- libkml=1.3.0=he250239_1021
- liblapack=3.9.0=25_osxarm64_openblas
- liblapacke=3.9.0=25_osxarm64_openblas
- libllvm14=14.0.6=hd1a9a77_4
- libllvm17=17.0.6=h5090b49_2
- libllvm19=19.1.2=haf57ff0_0
- libmamba=1.5.10=h66a2e1b_1
- libmambapy=1.5.10=py311h2e2787a_1
- libnetcdf=4.9.2=nompi_he469be0_114
- libnghttp2=1.64.0=h6d7220d_0
- libntlm=1.4=h3422bc3_1002
- libopenblas=0.3.28=openmp_h517c56d_0
- libpng=1.6.44=hc14010f_0
- libpq=17.0=h9fd3c6c_4
- libprotobuf=5.27.5=h53f8970_2
- libre2-11=2024.07.02=h2348fd5_1
- librttopo=1.1.0=ha2cf0f4_17
- libsodium=1.0.20=h99b78c6_0
- libsolv=0.7.30=h6c9b7f8_0
- libspatialindex=2.0.0=h00cdb27_0
- libspatialite=5.1.0=hffd3212_11
- libsqlite=3.47.0=hbaaea75_0
- libssh2=1.11.0=h7a5bd25_0
- libthrift=0.21.0=h64651cc_0
- libtiff=4.7.0=hfce79cd_1
- libtool=2.4.7=h00cdb27_1
- libutf8proc=2.8.0=h1a8c8d9_0
- libwebp=1.4.0=h54798ee_0
- libwebp-base=1.4.0=h93a5062_0
- libxcb=1.17.0=hdb1d25a_0
- libxml2=2.12.7=h01dff8b_4
- libxslt=1.1.39=h223e5b9_0
- libzip=1.11.1=hfc4440f_0
- libzlib=1.3.1=h8359307_2
- llist=0.7.1=py311hd6ee22a_3
- llvm-openmp=19.1.2=hb52a8e5_0
- lockfile=0.12.2=py_1
- logmuse=0.2.8=pyhd8ed1ab_0
- lxml=5.3.0=py311h96511b9_1
- lz4-c=1.9.4=hb7217d7_0
- lzo=2.10=h93a5062_1001
- mamba=1.5.10=py311hb045da1_1
- mapclassify=2.8.1=pyhd8ed1ab_0
- markdown-it-py=3.0.0=pyhd8ed1ab_0
- markupsafe=3.0.2=py311h56c23cb_0
- matplotlib=3.9.2=py311ha1ab1f8_1
- matplotlib-base=3.9.2=py311hbe3227e_1
- matplotlib-inline=0.1.7=pyhd8ed1ab_0
- mdurl=0.1.2=pyhd8ed1ab_0
- memory_profiler=0.61.0=pyhd8ed1ab_0
- menuinst=2.1.2=py311h267d04e_1
- minizip=4.0.7=h27ee973_0
- mistune=3.0.2=pyhd8ed1ab_0
- more-itertools=10.5.0=pyhd8ed1ab_0
- msgpack-python=1.1.0=py311h2c37856_0
- multidict=6.1.0=py311h30e7462_1
- munch=4.0.0=pyhd8ed1ab_0
- munkres=1.1.4=pyh9f0ad1d_0
- mypy_extensions=1.0.0=pyha770c72_0
- natsort=8.4.0=pyhd8ed1ab_0
- nbclient=0.10.0=pyhd8ed1ab_0
- nbconvert=7.16.4=hd8ed1ab_1
- nbconvert-core=7.16.4=pyhd8ed1ab_1
- nbconvert-pandoc=7.16.4=hd8ed1ab_1
- nbformat=5.10.4=pyhd8ed1ab_0
- ncbi-datasets-cli=16.33.0=hce30654_0
- ncurses=6.5=h7bae524_1
- nest-asyncio=1.6.0=pyhd8ed1ab_0
- networkx=3.4=pyhd8ed1ab_0
- nspr=4.36=h5833ebf_0
- nss=3.106=h6f44f80_0
- numpy=1.26.4=py311h7125741_0
- oauth2client=4.1.3=py_0
- openai=1.52.2=pyhd8ed1ab_0
- openjpeg=2.5.2=h9f1df11_0
- openldap=2.6.8=h50f2afc_0
- openssl=3.3.2=h8359307_0
- orc=2.0.2=h4a9587e_1
- packaging=24.1=pyhd8ed1ab_0
- pandas=1.5.3=py311h4eec4a9_1
- pandoc=3.5=hce30654_0
- pandocfilters=1.5.0=pyhd8ed1ab_0
- parallel=20240922=hce30654_0
- parso=0.8.4=pyhd8ed1ab_0
- patch-ng=1.18.0=pyhd8ed1ab_0
- pathspec=0.12.1=pyhd8ed1ab_0
- patsy=0.5.6=pyhd8ed1ab_0
- pcre2=10.44=h297a79d_2
- peppy=0.40.7=pyhd8ed1ab_0
- perl=5.32.1=7_h4614cfb_perl5
- pexpect=4.9.0=pyhd8ed1ab_0
- pickleshare=0.7.5=py_1003
- pillow=11.0.0=py311h3894ae9_0
- pip=24.2=pyh8b19718_1
- pixman=0.43.4=hebf3989_0
- pkginfo=1.11.2=pyhd8ed1ab_0
- pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1
- plac=1.4.3=pyhd8ed1ab_0
- platformdirs=4.3.6=pyhd8ed1ab_0
- plotly=5.24.1=pyhd8ed1ab_0
- pluggy=1.5.0=pyhd8ed1ab_0
- pluginbase=1.0.1=pyhd8ed1ab_0
- ply=3.11=pyhd8ed1ab_2
- poetry=1.8.4=osx_pyh534df25_0
- poetry-core=1.9.1=pyhd8ed1ab_0
- poetry-plugin-export=1.8.0=pyhd8ed1ab_0
- polars=1.11.0=py311h6f9c410_0
- pooch=1.8.2=pyhd8ed1ab_0
- poppler-data=0.4.12=hd8ed1ab_0
- postgresql=17.0=h25379d5_4
- prettytable=3.11.0=pyhd8ed1ab_0
- proj=9.5.0=h61a8e3e_0
- prompt-toolkit=3.0.48=pyha770c72_0
- prompt_toolkit=3.0.48=hd8ed1ab_0
- propcache=0.2.0=py311h460d6c5_2
- protobuf=5.27.5=py311h3f08180_0
- psutil=6.1.0=py311hae2e1ce_0
- psycopg2=2.9.9=py311h057640d_2
- pthread-stubs=0.4=hd74edd7_1002
- ptyprocess=0.7.0=pyhd3deb0d_0
- pulp=2.8.0=py311h267d04e_0
- pure_eval=0.2.3=pyhd8ed1ab_0
- pyasn1=0.6.1=pyhd8ed1ab_1
- pyasn1-modules=0.4.1=pyhd8ed1ab_0
- pybind11-abi=4=hd8ed1ab_3
- pycodestyle=2.12.1=pyhd8ed1ab_0
- pycosat=0.6.6=py311heffc1b2_0
- pycountry=24.6.1=pyhd8ed1ab_0
- pycparser=2.22=pyhd8ed1ab_0
- pydantic=2.9.2=pyhd8ed1ab_0
- pydantic-core=2.23.4=py311h481aa64_0
- pyflakes=3.2.0=pyhd8ed1ab_0
- pygments=2.18.0=pyhd8ed1ab_0
- pyjwt=2.9.0=pyhd8ed1ab_1
- pympler=1.1=pyhd8ed1ab_0
- pynacl=1.5.0=py311h460d6c5_4
- pyopenssl=24.2.1=pyhd8ed1ab_2
- pyparsing=3.2.0=pyhd8ed1ab_1
- pyproj=3.7.0=py311hb4b81e0_0
- pyproject_hooks=1.2.0=pyh7850678_0
- pyrsistent=0.20.0=py311h460d6c5_1
- pysocks=1.7.1=pyha2e5f31_6
- pytest=8.3.3=pyhd8ed1ab_0
- python=3.11.10=hc51fdd5_3_cpython
- python-build=1.2.2.post1=pyhff2d567_0
- python-dateutil=2.9.0=pyhd8ed1ab_0
- python-dotenv=1.0.1=pyhd8ed1ab_0
- python-duckdb=1.1.2=py311h6885ffc_1
- python-fastjsonschema=2.20.0=pyhd8ed1ab_0
- python-installer=0.7.0=pyhd8ed1ab_0
- python-irodsclient=2.1.0=pyhd8ed1ab_0
- python-tzdata=2024.2=pyhd8ed1ab_0
- python_abi=3.11=5_cp311
- pytz=2024.2=pyhd8ed1ab_0
- pyu2f=0.1.5=pyhd8ed1ab_0
- pyyaml=6.0.2=py311h460d6c5_1
- pyzmq=26.2.0=py311h730b646_3
- qhull=2020.2=h420ef59_5
- ratelimiter=1.2.0=py_1002
- re2=2024.07.02=hcd0e937_1
- readline=8.2=h92ec313_1
- referencing=0.35.1=pyhd8ed1ab_0
- regex=2024.9.11=py311h460d6c5_0
- reproc=14.2.4.post0=h93a5062_1
- reproc-cpp=14.2.4.post0=h965bd2d_1
- requests=2.32.3=pyhd8ed1ab_0
- requests-toolbelt=1.0.0=pyhd8ed1ab_0
- reretry=0.11.8=pyhd8ed1ab_0
- rich=13.9.3=pyhd8ed1ab_0
- rpds-py=0.20.0=py311h481aa64_1
- rsa=4.9=pyhd8ed1ab_0
- rtree=1.3.0=py311hc46b6d3_2
- ruamel.yaml=0.18.6=py311hae2e1ce_1
- ruamel.yaml.clib=0.2.8=py311hae2e1ce_1
- ruff=0.7.1=py311ha7de580_0
- s3transfer=0.10.3=pyhd8ed1ab_0
- scikit-learn=1.5.2=py311h9e23f0f_1
- scipy=1.14.1=py311hf1db568_1
- seaborn=0.13.2=hd8ed1ab_2
- seaborn-base=0.13.2=pyhd8ed1ab_2
- setuptools=75.1.0=pyhd8ed1ab_0
- setuptools-scm=8.1.0=pyhd8ed1ab_0
- shapely=2.0.6=py311hac502b4_2
- shellingham=1.5.4=pyhd8ed1ab_0
- six=1.16.0=pyh6c4a22f_0
- slack-sdk=3.33.2=pyha770c72_0
- slack_sdk=3.33.2=hd8ed1ab_0
- slacker=0.14.0=py_0
- smart_open=7.0.5=pyhd8ed1ab_1
- smmap=5.0.0=pyhd8ed1ab_0
- snakefmt=0.10.2=pyhdfd78af_0
- snakemake=8.24.1=hdfd78af_0
- snakemake-interface-common=1.17.4=pyhdfd78af_0
- snakemake-interface-executor-plugins=9.3.2=pyhdfd78af_0
- snakemake-interface-report-plugins=1.1.0=pyhdfd78af_0
- snakemake-interface-storage-plugins=3.3.0=pyhdfd78af_0
- snakemake-minimal=8.24.1=pyhdfd78af_0
- snappy=1.2.1=hd02b534_0
- sniffio=1.3.1=pyhd8ed1ab_0
- snipit=1.2=pyhdfd78af_0
- sortedcontainers=2.4.0=pyhd8ed1ab_0
- soupsieve=2.5=pyhd8ed1ab_1
- spdlog=1.14.1=h6d8af72_1
- sqlite=3.47.0=hcd14bea_0
- stack_data=0.6.2=pyhd8ed1ab_0
- statsmodels=0.14.4=py311h0f07fe1_0
- stone=3.3.8=pyhd8ed1ab_0
- stopit=1.1.2=py_0
- tabulate=0.9.0=pyhd8ed1ab_1
- tenacity=9.0.0=pyhd8ed1ab_0
- threadpoolctl=3.5.0=pyhc1e730c_0
- throttler=1.2.2=pyhd8ed1ab_0
- tiledb=2.26.2=h66ea1f1_4
- tinycss2=1.4.0=pyhd8ed1ab_0
- tk=8.6.13=h5083fa2_1
- toml=0.10.2=pyhd8ed1ab_0
- tomli=2.0.2=pyhd8ed1ab_0
- tomlkit=0.13.2=pyha770c72_0
- toolz=1.0.0=pyhd8ed1ab_0
- toposort=1.10=pyhd8ed1ab_0
- tornado=6.4.1=py311h460d6c5_1
- tqdm=4.66.6=pyhd8ed1ab_0
- traitlets=5.14.3=pyhd8ed1ab_0
- treetime=0.11.4=pyhdfd78af_0
- trove-classifiers=2024.10.21.16=pyhd8ed1ab_0
- truststore=0.10.0=pyhd8ed1ab_0
- tsv-utils=2.2.3=h99b78c6_7
- typed-ast=1.5.5=py311heffc1b2_1
- typer=0.12.5=pyhd8ed1ab_0
- typer-slim=0.12.5=pyhd8ed1ab_0
- typer-slim-standard=0.12.5=hd8ed1ab_0
- typing=3.10.0.0=pyhd8ed1ab_1
- typing-extensions=4.12.2=hd8ed1ab_0
- typing_extensions=4.12.2=pyha770c72_0
- tzcode=2024b=hd74edd7_0
- tzdata=2024b=hc8b5060_0
- ubiquerg=0.8.0=pyhd8ed1ab_0
- unicodedata2=15.1.0=py311hae2e1ce_1
- untokenize=0.1.1=pyhd8ed1ab_1
- uriparser=0.9.8=h00cdb27_0
- uritemplate=4.1.1=pyhd8ed1ab_0
- urllib3=1.26.19=pyhd8ed1ab_0
- userpath=1.7.0=pyhd8ed1ab_0
- veracitools=0.1.3=py_0
- virtualenv=20.27.0=pyhd8ed1ab_0
- wcwidth=0.2.13=pyhd8ed1ab_0
- webencodings=0.5.1=pyhd8ed1ab_2
- werkzeug=3.0.6=pyhd8ed1ab_0
- wheel=0.44.0=pyhd8ed1ab_0
- wrapt=1.16.0=py311h460d6c5_1
- xattr=1.1.0=py311h460d6c5_1
- xerces-c=3.3.0=hd62221f_0
- xlrd=2.0.1=pyhd8ed1ab_3
- xlsx2csv=0.8.3=pyhd8ed1ab_0
- xmltodict=0.14.2=pyhd8ed1ab_0
- xorg-kbproto=1.0.7=hd74edd7_1003
- xorg-libice=1.1.1=hd74edd7_1
- xorg-libsm=1.2.4=hd74edd7_1
- xorg-libx11=1.8.10=h2321a68_0
- xorg-libxau=1.0.11=hd74edd7_1
- xorg-libxdmcp=1.1.5=hd74edd7_0
- xorg-libxext=1.3.6=hd74edd7_0
- xorg-libxrender=0.9.11=hd74edd7_1
- xorg-libxt=1.3.0=hd74edd7_2
- xorg-renderproto=0.11.1=hd74edd7_1003
- xorg-xextproto=7.3.0=hd74edd7_1004
- xorg-xorgproto=2024.1=hd74edd7_1
- xorg-xproto=7.0.31=hd74edd7_1008
- xsdata=24.9=pyhd8ed1ab_0
- xyzservices=2024.9.0=pyhd8ed1ab_0
- xz=5.2.6=h57fd34a_0
- yaml=0.2.5=h3422bc3_2
- yaml-cpp=0.8.0=h13dd4ca_0
- yarl=1.16.0=py311hae2e1ce_0
- yte=1.5.4=pyha770c72_0
- zeromq=4.3.5=h9f5b81c_6
- zipp=3.20.2=pyhd8ed1ab_0
- zlib=1.3.1=h8359307_2
- zstandard=0.23.0=py311ha60cc69_1
- zstd=1.5.6=hb46c0d2_0

~/.condarc

$ cat ~/.condarc
always_yes: true
show_channel_urls: true
solver: libmamba
changeps1: False
channels:
  - bioconda
  - conda-forge
  - nodefaults
channel_priority: strict

$ cat ~/.mambarc
repodata_use_zst: true
channels:
- conda-forge
- bioconda
jjerphan commented 6 days ago

Thank you for the report.

I have not been able to reproduce the issue as of now: I am not using macOS, and I guess this issue might be quite specific to your macOS environment.

jjerphan commented 4 days ago

Currently you have (at least) two installations of micromamba and mamba.

This is unclear and likely causing problems (duplication of aliases, root prefixes, etc.), and we recommend coming up with a single installation of mamba and micromamba first.

If you still meet the problem then, feel free to reopen this issue.