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Issue Description:
During the setup phase of the CI workflow, the job failed with the following error message:
For python3.9:
Installed versionsVersion 3.9 was not found in the local cacheError: 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=c99lib/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 msprimeBuilding wheel for dendropy (pyproject.toml): startedBuilding 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=82e583b8bd45f2e3743fa76245057c2fb7d856af6129e43e1b92a05c1afd00f1Stored in directory: /Users/runner/Library/Caches/pip/wheels/2c/c8/56/a077856a8b16234966f2f32da8c60d8083bd8e131f4171aca9Building wheel for docopt (pyproject.toml): startedBuilding 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=497aa1707f722ce1a40e09bb1bbee5ce198199224a6926a282f17b76ca1bc95fStored in directory: /Users/runner/Library/Caches/pip/wheels/fc/ab/d4/5da2067ac95b36618c629a5f93f809425700506f72c9732facBuilding wheel for asciitree (pyproject.toml): startedBuilding 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=d333b36d0312c91b6c72d00e35d1dfd0529e0ac37849ab2661d2b6de74be7055Stored in directory: /Users/runner/Library/Caches/pip/wheels/7f/4e/be/1171b40f43b918087657ec57cf3b81fa1a2e027d8755baa184Successfully built tskit dendropy docopt asciitreeFailed to build msprimeERROR: Could not build wheels for msprime, which is required to install pyproject.toml-based projectsNotice: A new release of pip is available: 23.0.1 -> 24.0Notice: To update, run: python -m pip install --upgrade pipError: 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-1.5.0rootdir: /Users/runner/work/phylokit/phylokit, configfile: pyproject.toml, testpaths: testsplugins: xdist-2.5.0, forked-1.6.0collected 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_modulereturn _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.
Issue Description:
During the setup phase of the CI workflow, the job failed with the following error message:
For python3.9:
For python3.10:
For python3.11
Temporary Fix:
The text was updated successfully, but these errors were encountered: