Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

CI Failure on macos-latest #44

Closed
Billyzhang1229 opened this issue Apr 29, 2024 · 0 comments
Closed

CI Failure on macos-latest #44

Billyzhang1229 opened this issue Apr 29, 2024 · 0 comments

Comments

@Billyzhang1229
Copy link
Contributor

Issue Description:
During the setup phase of the CI workflow, the job failed with the following error message:

For python3.9:

Installed versions
Version 3.9 was not found in the local cache
Error: The version '3.9' with architecture 'arm64' was not found for macOS 14.4.1.

For python3.10:

clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -Ilwt_interface -Ilib -Igit-submodules/tskit/c -Igit-submodules/tskit/c/tskit -Igit-submodules/tskit/c/subprojects/kastore -I/private/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T/pip-build-env-0uh53mv5/overlay/lib/python3.10/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c lib/fenwick.c -o build/temp.macosx-10.9-universal2-cpython-310/lib/fenwick.o -std=c99
      lib/fenwick.c:31:10: fatal error: 'gsl/gsl_math.h' file not found
      #include <gsl/gsl_math.h>
               ^~~~~~~~~~~~~~~~
      1 error generated.
      error: command '/usr/bin/clang' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for msprime
  Building wheel for dendropy (pyproject.toml): started
  Building wheel for dendropy (pyproject.toml): finished with status 'done'
  Created wheel for dendropy: filename=DendroPy-4.5.2-py3-none-any.whl size=452924 sha256=82e583b8bd45f2e3743fa76245057c2fb7d856af6129e43e1b92a05c1afd00f1
  Stored in directory: /Users/runner/Library/Caches/pip/wheels/2c/c8/56/a077856a8b16234966f2f32da8c60d8083bd8e131f4171aca9
  Building wheel for docopt (pyproject.toml): started
  Building wheel for docopt (pyproject.toml): finished with status 'done'
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13706 sha256=497aa1707f722ce1a40e09bb1bbee5ce198199224a6926a282f17b76ca1bc95f
  Stored in directory: /Users/runner/Library/Caches/pip/wheels/fc/ab/d4/5da2067ac95b36618c629a5f93f809425700506f72c9732fac
  Building wheel for asciitree (pyproject.toml): started
  Building wheel for asciitree (pyproject.toml): finished with status 'done'
  Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5034 sha256=d333b36d0312c91b6c72d00e35d1dfd0529e0ac37849ab2661d2b6de74be7055
  Stored in directory: /Users/runner/Library/Caches/pip/wheels/7f/4e/be/1171b40f43b918087657ec57cf3b81fa1a2e027d8755baa184
Successfully built tskit dendropy docopt asciitree
Failed to build msprime
ERROR: Could not build wheels for msprime, which is required to install pyproject.toml-based projects

Notice:  A new release of pip is available: 23.0.1 -> 24.0
Notice:  To update, run: python -m pip install --upgrade pip
Error: Process completed with exit code 1.

For python3.11

Run coverage run --source=phylokit -m pytest -x -n0
============================= test session starts ==============================
platform darwin -- Python 3.[11](https://github.com/jeromekelleher/phylokit/actions/runs/8833654919/job/24253475210#step:6:12).9, pytest-7.1.2, pluggy-1.5.0
rootdir: /Users/runner/work/phylokit/phylokit, configfile: pyproject.toml, testpaths: tests
plugins: xdist-2.5.0, forked-1.6.0
collected 50 items / 1 error

==================================== ERRORS ====================================
____________________ ERROR collecting tests/test_convert.py ____________________
ImportError while importing test module '/Users/runner/work/phylokit/phylokit/tests/test_convert.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py:[12](https://github.com/jeromekelleher/phylokit/actions/runs/8833654919/job/24253475210#step:6:13)6: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_convert.py:1: in <module>
    import msprime
/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/msprime/__init__.py:28: in <module>
    from msprime._msprime import (
E   ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/msprime/_msprime.cpython-311-darwin.so, 0x0002): symbol not found in flat namespace '_gsl_rng_default'
=========================== short test summary info ============================
ERROR tests/test_convert.py
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
=============================== 1 error in 6.86s ===============================
Error: Process completed with exit code 1.

Temporary Fix:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant