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.

Sign up for GitHub

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

Jump to bottom

Build test fails for macOS with Python 3.9 #216

Open
RalfG opened this issue Mar 5, 2024 · 0 comments
Open

Build test fails for macOS with Python 3.9 #216

RalfG opened this issue Mar 5, 2024 · 0 comments
Labels
deployment

Comments

@RalfG
Copy link
Member

RalfG commented Mar 5, 2024 •
edited
Loading

See https://github.com/compomics/ms2pip/actions/runs/7845409300/job/22261596464

 Building cp39-macosx_x86_64 wheel
CPython 3.9 macOS x86_64

Installing Python cp39...
                                                             ✓ 34.86s
Setting up build environment...
                                                              ✓ 6.62s
Installing build tools...
                                                              ✓ 3.44s
Building wheel...
                                                            ✓ 301.82s
Repairing wheel...
                                                             ✓ 13.68s
Testing wheel...
  
  + pip install virtualenv -c /Users/runner/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/site-packages/cibuildwheel/resources/constraints-python39.txt
  Collecting virtualenv
    Using cached virtualenv-20.10.0-py2.py3-none-any.whl (5.6 MB)
  Collecting backports.entry-points-selectable>=1.0.4
    Using cached backports.entry_points_selectable-1.1.1-py2.py3-none-any.whl (6.2 kB)
  Collecting six<2,>=1.9.0
    Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
  Collecting distlib<1,>=0.3.1
    Using cached distlib-0.3.4-py2.py3-none-any.whl (461 kB)
  Collecting filelock<4,>=3.2
    Using cached filelock-3.4.0-py3-none-any.whl (9.8 kB)
  Collecting platformdirs<3,>=2
    Using cached platformdirs-2.4.0-py3-none-any.whl (14 kB)
  Installing collected packages: six, platformdirs, filelock, distlib, backports.entry-points-selectable, virtualenv
  Successfully installed backports.entry-points-selectable-1.1.1 distlib-0.3.4 filelock-3.4.0 platformdirs-2.4.0 six-1.16.0 virtualenv-20.10.0
  + python -m virtualenv --no-download /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h
  created virtual environment CPython3.9.9.final.0-64 in 1771ms
    creator CPython3Posix(dest=/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h, clear=False, no_vcs_ignore=False, global=False)
    seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/Users/runner/Library/Application Support/virtualenv)
      added seed packages: pip==21.3.1, setuptools==58.3.0, wheel==0.37.0
    activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator
  + which python
  /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/bin/python
  + pip install /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/cibuildwheeltxn1voh5/repaired_wheel/ms2pip-3.13.0-cp39-cp39-macosx_10_9_x86_64.whl
  Processing /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/cibuildwheeltxn1voh5/repaired_wheel/ms2pip-3.13.0-cp39-cp39-macosx_10_9_x86_64.whl
  Collecting pyteomics<5,>=3.5
    Using cached pyteomics-4.7.1-py2.py3-none-any.whl (236 kB)
  Collecting xgboost<2,>=1.3
    Using cached xgboost-1.7.6-py3-none-macosx_10_15_x86_64.macosx_11_0_x86_64.macosx_12_0_x86_64.whl (1.8 MB)
  Collecting tables>=3.4
    Downloading tables-3.9.2-cp39-cp39-macosx_10_9_x86_64.whl (7.4 MB)
  Collecting pandas<2,>=1
    Downloading pandas-1.5.3-cp39-cp39-macosx_10_9_x86_64.whl (12.0 MB)
  Collecting spectrum-utils==0.3.5
    Using cached spectrum_utils-0.3.5-py3-none-any.whl (24 kB)
  Collecting biopython<2,>=1.74
    Downloading biopython-1.83-cp39-cp39-macosx_10_9_x86_64.whl (2.7 MB)
  Collecting lxml>=4
    Downloading lxml-5.1.0-cp39-cp39-macosx_10_9_x86_64.whl (4.7 MB)
  Collecting pydantic<2,>=1.10
    Downloading pydantic-1.10.14-cp39-cp39-macosx_10_9_x86_64.whl (2.9 MB)
  Collecting rich>=13
    Using cached rich-13.7.1-py3-none-any.whl (240 kB)
  Collecting tqdm<5,>=4
    Using cached tqdm-4.66.2-py3-none-any.whl (78 kB)
  Collecting sqlalchemy<2,>=1.3
    Downloading SQLAlchemy-1.4.52-cp39-cp39-macosx_11_0_x86_64.whl (1.6 MB)
  Collecting click<9,>=7
    Using cached click-8.1.7-py3-none-any.whl (97 kB)
  Collecting matplotlib>=3.0
    Downloading matplotlib-3.8.3-cp39-cp39-macosx_10_12_x86_64.whl (7.6 MB)
  Collecting numpy<2,>=1.16
    Downloading numpy-1.26.4-cp39-cp39-macosx_10_9_x86_64.whl (20.6 MB)
  Collecting tomlkit<1,>=0.5
    Using cached tomlkit-0.12.4-py3-none-any.whl (37 kB)
  Collecting numba>=0.47
    Downloading numba-0.59.0-cp39-cp39-macosx_10_9_x86_64.whl (2.6 MB)
  Collecting importlib-resources>=3.2.0
    Using cached importlib_resources-6.1.2-py3-none-any.whl (34 kB)
  Collecting python-dateutil>=2.7
    Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
  Collecting contourpy>=1.0.1
    Downloading contourpy-1.2.0-cp39-cp39-macosx_10_9_x86_64.whl (257 kB)
  Collecting packaging>=20.0
    Using cached packaging-23.2-py3-none-any.whl (53 kB)
  Collecting fonttools>=4.22.0
    Downloading fonttools-4.49.0-cp39-cp39-macosx_10_9_x86_64.whl (2.3 MB)
  Collecting pillow>=8
    Downloading pillow-10.2.0-cp39-cp39-macosx_10_10_x86_64.whl (3.5 MB)
  Collecting pyparsing>=2.3.1
    Using cached pyparsing-3.1.1-py3-none-any.whl (103 kB)
  Collecting kiwisolver>=1.3.1
    Downloading kiwisolver-1.4.5-cp39-cp39-macosx_10_9_x86_64.whl (68 kB)
  Collecting cycler>=0.10
    Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
  Collecting pytz>=2020.1
    Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB)
  Collecting typing-extensions>=4.2.0
    Using cached typing_extensions-4.10.0-py3-none-any.whl (33 kB)
  Collecting pygments<3.0.0,>=2.13.0
    Using cached pygments-2.17.2-py3-none-any.whl (1.2 MB)
  Collecting markdown-it-py>=2.2.0
    Using cached markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
  Collecting greenlet!=0.4.17
    Downloading greenlet-3.0.3-cp39-cp39-macosx_11_0_universal2.whl (269 kB)
  Collecting numexpr>=2.6.2
    Downloading numexpr-2.9.0-cp39-cp39-macosx_10_9_x86_64.whl (102 kB)
  Collecting py-cpuinfo
    Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
  Collecting blosc2>=2.3.0
    Downloading blosc2-2.5.1-cp39-cp39-macosx_10_9_x86_64.whl (4.4 MB)
  Collecting scipy
    Downloading scipy-1.12.0-cp39-cp39-macosx_10_9_x86_64.whl (38.9 MB)
  Collecting ndindex>=1.4
    Downloading ndindex-1.8-py3-none-any.whl (91 kB)
  Collecting msgpack
    Downloading msgpack-1.0.8-cp39-cp39-macosx_10_9_x86_64.whl (88 kB)
  Collecting zipp>=3.1.0
    Using cached zipp-3.17.0-py3-none-any.whl (7.4 kB)
  Collecting mdurl~=0.1
    Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB)
  Collecting llvmlite<0.43,>=0.42.0dev0
    Downloading llvmlite-0.42.0-cp39-cp39-macosx_10_9_x86_64.whl (31.1 MB)
  Collecting six>=1.5
    Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
  Installing collected packages: zipp, six, numpy, python-dateutil, pyparsing, py-cpuinfo, pillow, packaging, ndindex, msgpack, mdurl, llvmlite, kiwisolver, importlib-resources, fonttools, cycler, contourpy, typing-extensions, scipy, pytz, pyteomics, pygments, numexpr, numba, matplotlib, markdown-it-py, greenlet, blosc2, xgboost, tqdm, tomlkit, tables, sqlalchemy, spectrum-utils, rich, pydantic, pandas, lxml, click, biopython, ms2pip
  Successfully installed biopython-1.83 blosc2-2.5.1 click-8.1.7 contourpy-1.2.0 cycler-0.12.1 fonttools-4.49.0 greenlet-3.0.3 importlib-resources-6.1.2 kiwisolver-1.4.5 llvmlite-0.42.0 lxml-5.1.0 markdown-it-py-3.0.0 matplotlib-3.8.3 mdurl-0.1.2 ms2pip-3.13.0 msgpack-1.0.8 ndindex-1.8 numba-0.59.0 numexpr-2.9.0 numpy-1.26.4 packaging-23.2 pandas-1.5.3 pillow-10.2.0 py-cpuinfo-9.0.0 pydantic-1.10.14 pygments-2.17.2 pyparsing-3.1.1 pyteomics-4.7.1 python-dateutil-2.9.0.post0 pytz-2024.1 rich-13.7.1 scipy-1.12.0 six-1.16.0 spectrum-utils-0.3.5 sqlalchemy-1.4.52 tables-3.9.2 tomlkit-0.12.4 tqdm-4.66.2 typing-extensions-4.10.0 xgboost-1.7.6 zipp-3.17.0
  + pip install pytest
  Collecting pytest
    Using cached pytest-8.0.2-py3-none-any.whl (333 kB)
  Collecting exceptiongroup>=1.0.0rc8
    Using cached exceptiongroup-1.2.0-py3-none-any.whl (16 kB)
  Collecting iniconfig
    Using cached iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
  Collecting tomli>=1.0.0
    Using cached tomli-2.0.1-py3-none-any.whl (12 kB)
  Requirement already satisfied: packaging in /private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages (from pytest) (23.2)
  Collecting pluggy<2.0,>=1.3.0
    Using cached pluggy-1.4.0-py3-none-any.whl (20 kB)
  Installing collected packages: tomli, pluggy, iniconfig, exceptiongroup, pytest
  Successfully installed exceptiongroup-1.2.0 iniconfig-2.0.0 pluggy-1.4.0 pytest-8.0.2 tomli-2.0.1
  +  pytest /Users/runner/work/ms2pip/ms2pip/tests
  ============================= test session starts ==============================
  platform darwin -- Python 3.9.9, pytest-8.0.2, pluggy-1.4.0
  rootdir: /Users/runner/work/ms2pip/ms2pip
  collected 20 items
  
  work/ms2pip/ms2pip/tests/test_config_parser.py ...                       [ 15%]
  work/ms2pip/ms2pip/tests/test_fasta2speclib.py ...                       [ 30%]
  Fatal Python error: Illegal instruction
  
  Current thread 0x000000010d702600 (most recent call first):
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/tables/node.py", line 246 in __init__
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/tables/leaf.py", line 264 in __init__
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/tables/array.py", line 172 in __init__
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/tables/file.py", line 1119 in create_array
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pandas/io/pytables.py", line 3126 in write_array
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pandas/io/pytables.py", line 2930 in write_index
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pandas/io/pytables.py", line 3249 in write
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pandas/io/pytables.py", line 1776 in _write_to_group
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pandas/io/pytables.py", line 1123 in put
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pandas/io/pytables.py", line 283 in <lambda>
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pandas/io/pytables.py", line 301 in to_hdf
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pandas/core/generic.py", line 2799 in to_hdf
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/ms2pip/ms2pipC.py", line 1010 in _write_vector_file
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/ms2pip/ms2pipC.py", line 823 in run
    File "/Users/runner/work/ms2pip/ms2pip/tests/test_features.py", line 47 in test_dummy_spectrum
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/python.py", line 194 in pytest_pyfunc_call
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_callers.py", line 102 in _multicall
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_manager.py", line 119 in _hookexec
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_hooks.py", line 501 in __call__
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/python.py", line 1831 in runtest
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/runner.py", line 170 in pytest_runtest_call
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_callers.py", line 102 in _multicall
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_manager.py", line 119 in _hookexec
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_hooks.py", line 501 in __call__
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/runner.py", line 263 in <lambda>
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/runner.py", line 342 in from_call
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/runner.py", line 262 in call_runtest_hook
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/runner.py", line 223 in call_and_report
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/runner.py", line 134 in runtestprotocol
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/runner.py", line 115 in pytest_runtest_protocol
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_callers.py", line 102 in _multicall
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_manager.py", line 119 in _hookexec
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_hooks.py", line 501 in __call__
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/main.py", line 352 in pytest_runtestloop
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_callers.py", line 102 in _multicall
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_manager.py", line 119 in _hookexec
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_hooks.py", line 501 in __call__
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/main.py", line 327 in _main
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/main.py", line 273 in wrap_session
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/main.py", line 320 in pytest_cmdline_main
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_callers.py", line 102 in _multicall
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_manager.py", line 119 in _hookexec
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/pluggy/_hooks.py", line 501 in __call__
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/config/__init__.py", line 175 in main
    File "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/lib/python3.9/site-packages/_pytest/config/__init__.py", line 198 in console_main
    File "/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpj8wzmu2h/bin/pytest", line 8 in <module>
  Error: Command  pytest /Users/runner/work/ms2pip/ms2pip/tests failed with code -4. None
  work/ms2pip/ms2pip/tests/test_features.py ::endgroup::Testing wheel...
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
deployment
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@RalfG