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Conda setup failing on creation in github CI workflow #292

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jhdark opened this issue Oct 11, 2023 · 5 comments
Open

Conda setup failing on creation in github CI workflow #292

jhdark opened this issue Oct 11, 2023 · 5 comments

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@jhdark
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jhdark commented Oct 11, 2023

Hi all, I can't seem to have conda working reliably in a github ci workflow, I assume it has something to do with using mamba too? I do need this to install a package later down the line. But, the initialisation seems to fail occasionally. Heres the .yml file I use and the error produced

on: [pull_request, push]

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout code
      uses: actions/checkout@v2

    - name: Set up Conda
      uses: conda-incubator/setup-miniconda@v2
      with:
        activate-environment: myenv
        mamba-version: "*"
        channels: conda-forge, defaults

Error:

  /usr/share/miniconda/condabin/mamba create --name myenv
  Warning: Traceback (most recent call last):
    File "/usr/share/miniconda/condabin/mamba", line 7, in <module>
  
  Traceback (most recent call last):
    File "/usr/share/miniconda/condabin/mamba", line 7, in <module>
  Warning:     from mamba.mamba import main
    File "/usr/share/miniconda/lib/python3.11/site-packages/mamba/mamba.py", line 49, in <module>
      import libmambapy as api
    File "/usr/share/miniconda/lib/python3.11/site-packages/libmambapy/__init__.py", line 7, in <module>
      raise e
    File "/usr/share/miniconda/lib/python3.11/site-packages/libmambapy/__init__.py", line 4, in <module>
      from libmambapy.bindings import *  # noqa: F401,F403
      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  ImportError: /usr/share/miniconda/lib/python3.11/site-packages/libmambapy/../../../libmamba.so.2: undefined symbol: solver_ruleinfo2str, version SOLV_1.0
  
      from mamba.mamba import main
    File "/usr/share/miniconda/lib/python3.11/site-packages/mamba/mamba.py", line 49, in <module>
      import libmambapy as api
    File "/usr/share/miniconda/lib/python3.11/site-packages/libmambapy/__init__.py", line 7, in <module>
      raise e
    File "/usr/share/miniconda/lib/python3.11/site-packages/libmambapy/__init__.py", line 4, in <module>
      from libmambapy.bindings import *  # noqa: F401,F403
      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  ImportError: /usr/share/miniconda/lib/python3.11/site-packages/libmambapy/../../../libmamba.so.2: undefined symbol: solver_ruleinfo2str, version SOLV_1.0

Error: The process '/usr/share/miniconda/condabin/mamba' failed with exit code 1```
@RemDelaporteMathurin
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The complete action run is available here

@tobiasdiez tobiasdiez mentioned this issue Oct 16, 2023
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@nikosavola nikosavola mentioned this issue Oct 17, 2023
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@tobiasdiez
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tobiasdiez commented Oct 18, 2023 •
edited

As a workaround, you can use mamba from miniforge by replacing mamba-version: '*' with

          miniforge-version: latest
          use-mamba: true
          channels: conda-forge

@jhdark
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jhdark commented Oct 18, 2023

This seems to work great thanks @tobiasdiez !

vbraun pushed a commit to vbraun/sage that referenced this issue Oct 19, 2023
sagemathgh-36468: Fix mamba install in conda ci workflow
acb1953 
    
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Mamba currently has problems with dependencies installed from other
channels (libarchive/libarchive#1857,
conda-incubator/setup-miniconda#292,
conda-forge/libarchive-feedstock#69), see eg h
ttps://github.com/sagemath/sage/actions/runs/6525067702/job/17717363515.

As workaround we use miniforge now (which comes with a preinstalled
mamba from conda-forge)

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### ⌛ Dependencies

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URL: sagemath#36468
Reported by: Tobias Diez
Reviewer(s): Isuru Fernando, Matthias Köppe
phelps-sg added a commit to phelps-sg/llm-cooperation that referenced this issue Oct 20, 2023
@phelps-sg
workaround for conda-incubator/setup-miniconda#292
fb1fa56
@dlcaballero16
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dlcaballero16 commented Oct 24, 2023 •
edited

So I am having a similar issue where I have an undefined symbol. According to Mamba documentation, it does not like having the defaults channel included. When looking at the action on github, the defaults channel still gets added in the Applying Initial Configuration step, though not sure why. Hope this info helps.

Edit: I have not tried using the workaround above yet

@goanpeca
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Indeed, it seems the defaults channel might be still leaking. Will take a look

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5 participants
@goanpeca @tobiasdiez @RemDelaporteMathurin @jhdark @dlcaballero16