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MacOS arm64 wheels fail with libdeflate error #252

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tomwhite opened this issue Sep 21, 2022 · 3 comments · Fixed by #253
Closed

MacOS arm64 wheels fail with libdeflate error #252

tomwhite opened this issue Sep 21, 2022 · 3 comments · Fixed by #253
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@tomwhite
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This has been happening since 0.30.14 (0.30.12 works fine). It looks like this is due to #231.

% pip install cyvcf2==0.30.16
Collecting cyvcf2==0.30.16
  Downloading cyvcf2-0.30.16-cp38-cp38-macosx_11_0_arm64.whl (1.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 2.1 MB/s eta 0:00:00
Collecting coloredlogs
  Using cached coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)
Collecting numpy
  Using cached numpy-1.23.3-cp38-cp38-macosx_11_0_arm64.whl (13.3 MB)
Collecting click
  Using cached click-8.1.3-py3-none-any.whl (96 kB)
Collecting humanfriendly>=9.1
  Using cached humanfriendly-10.0-py2.py3-none-any.whl (86 kB)
Installing collected packages: numpy, humanfriendly, click, coloredlogs, cyvcf2
Successfully installed click-8.1.3 coloredlogs-15.0.1 cyvcf2-0.30.16 humanfriendly-10.0 numpy-1.23.3
%  cyvcf2 --help                                          
Traceback (most recent call last):
  File "/Users/tom/miniforge3/envs/cyvcf-numpy-test-arm64/bin/cyvcf2", line 5, in <module>
    from cyvcf2.__main__ import cli
  File "/Users/tom/miniforge3/envs/cyvcf-numpy-test-arm64/lib/python3.8/site-packages/cyvcf2/__init__.py", line 1, in <module>
    from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
ImportError: dlopen(/Users/tom/miniforge3/envs/cyvcf-numpy-test-arm64/lib/python3.8/site-packages/cyvcf2/cyvcf2.cpython-38-darwin.so, 0x0002): symbol not found in flat namespace (_libdeflate_alloc_compressor)
@tomwhite tomwhite added the bug label Sep 21, 2022
@tomwhite
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I'm not sure how to fix this, so I'm looking at how to disable libdeflate for macos arm64.

@brentp
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brentp commented Sep 21, 2022

sounds good. where does libdeflate go on OSX? since

        CIBW_ENVIRONMENT: "CYTHONIZE=1 LIBDEFLATE=1 C_INCLUDE_PATH='/usr/local/include' LIBRARY_PATH='/usr/local/lib'"

in not sufficient.

@tomwhite
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I don't know 😄 The existing build works fine on macos x86, it's just on arm64 that libdeflate is not being found.

I've got a PR at #253.

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