Describe your issue.
Starting last night, I started seeing downstream CI testing failures on Ubuntu, across all Python versions tested (3.8, 3.9, 3.10, 3.11). One example is given here: https://github.com/MilesCranmer/PySR/actions/runs/5168482287. This installation method tests whether a conda-forge installed version of pysr (which has scipy as an indirect dependency) is working. I test both mamba and conda as well but this does not change the behavior. This is otherwise a very stable set of tests, with occasional failures on a single OS+Python version. But it is rare to see all Python versions fail in sync like this.
This might not be due to a change in scipy, but a change in a dependency that breaks the linkage to libstdc++. However, whatever change happened currently breaks the scipy build on ubuntu+conda, across all python versions.
These are the dependencies of PySR:
sympy
pandas
numpy
scikit_learn>=1.0.0
julia>=0.6.0
click>=7.0.0
setuptools>=50.0.0
Of these, only scikit-learn directly depends on scipy.
Reproducing Code Example
# (This is a GitHub action definition)
name: conda-forge
on:
schedule:
# Run at the 0th minute of the 10th hour (UTC).
# This means the job will run at 5am EST.
- cron: "0 10 * * *"
# This will automatically run on master branch only.
workflow_dispatch:
jobs:
conda_test:
runs-on: ${{ matrix.os }}
timeout-minutes: 60
defaults:
run:
shell: bash -l {0}
strategy:
fail-fast: false
matrix:
python-version: ['3.8', '3.9', '3.10', '3.11']
os: ['ubuntu-latest', 'macos-latest']
use-mamba: [true, false]
steps:
- name: "Set up Conda"
uses: conda-incubator/setup-miniconda@v2
with:
miniforge-variant: Mambaforge
miniforge-version: latest
auto-activate-base: true
python-version: ${{ matrix.python-version }}
activate-environment: pysr-test
- name: "Install pysr with mamba"
run: conda activate pysr-test && mamba install pysr
if: ${{ matrix.use-mamba }}
- name: "Install pysr with conda"
run: conda activate pysr-test && conda install pysr
if: ${{ !matrix.use-mamba }}
- name: "Run tests"
run: python -m pysr.test mainError message
Run python -m pysr.test main
python -m pysr.test main
shell: /usr/bin/bash -l {0}
env:
INPUT_RUN_POST: true
CONDA: /usr/share/miniconda3
CONDA_PKGS_DIR: /home/runner/conda_pkgs_dir
ERROR: Unable to dlopen(cxxpath) in parent!
Message: /usr/share/miniconda3/envs/pysr-test/lib/python3.10/site-packages/scipy/sparse/../../../../libstdc++.so.6GB?`�: cannot open shared object file: No such file or directoryAdditional info
Here is the recipe file that PySR uses:
https://github.com/conda-forge/pysr-feedstock/blob/6b5be685bf409af2304d18b94181db87c7c90843/recipe/meta.yaml#L28-L38
with the relevant conda dependencies here:
run:
- python
- pyjulia >=0.6.0
- julia
- numpy >=1.14.0
- pandas
- sympy
- scikit-learn >=1.0.0
- click >=7.0.0
- openlibm
- openspecfun
Describe your issue.
Starting last night, I started seeing downstream CI testing failures on Ubuntu, across all Python versions tested (3.8, 3.9, 3.10, 3.11). One example is given here: https://github.com/MilesCranmer/PySR/actions/runs/5168482287. This installation method tests whether a
conda-forgeinstalled version ofpysr(which hasscipyas an indirect dependency) is working. I test bothmambaandcondaas well but this does not change the behavior. This is otherwise a very stable set of tests, with occasional failures on a single OS+Python version. But it is rare to see all Python versions fail in sync like this.This might not be due to a change in
scipy, but a change in a dependency that breaks the linkage to libstdc++. However, whatever change happened currently breaks the scipy build on ubuntu+conda, across all python versions.These are the dependencies of PySR:
Of these, only scikit-learn directly depends on scipy.
Reproducing Code Example
Error message
Run python -m pysr.test main python -m pysr.test main shell: /usr/bin/bash -l {0} env: INPUT_RUN_POST: true CONDA: /usr/share/miniconda3 CONDA_PKGS_DIR: /home/runner/conda_pkgs_dir ERROR: Unable to dlopen(cxxpath) in parent! Message: /usr/share/miniconda3/envs/pysr-test/lib/python3.10/site-packages/scipy/sparse/../../../../libstdc++.so.6GB?`�: cannot open shared object file: No such file or directoryAdditional info
Here is the recipe file that PySR uses:
https://github.com/conda-forge/pysr-feedstock/blob/6b5be685bf409af2304d18b94181db87c7c90843/recipe/meta.yaml#L28-L38
with the relevant conda dependencies here: