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compomics / ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
https://ms2pip.readthedocs.io
Apache License 2.0
35 stars 18 forks source link

Build test fails for macOS with Python 3.9 #216

Open RalfG opened 5 months ago

RalfG commented 5 months ago

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...