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BROKEN: try to update htslib #278

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BROKEN: try to update htslib #278

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brentp
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@brentp brentp commented Aug 22, 2023

@tomwhite @ccwang002

I'm lost on trying to keep things building. Do either of you see how to fix this?

Right now, I get:

======================================================================
ERROR: cyvcf2 (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: cyvcf2
Traceback (most recent call last):
  File "/usr/lib/python3.10/unittest/loader.py", line 470, in _find_test_path
    package = self._get_module_from_name(name)
  File "/usr/lib/python3.10/unittest/loader.py", line 377, in _get_module_from_name
    __import__(name)
  File "/home/brentp/src/cyvcf2/cyvcf2/__init__.py", line 1, in <module>
    from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
ImportError: /home/brentp/src/cyvcf2/cyvcf2/cyvcf2.cpython-310-x86_64-linux-gnu.so: undefined symbol: rans_uncompress_O0_32x16_sse4

@ccwang002
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It seems that the errors are largely due to the compilation of CPU feature specific code in htscodecs submodule. My quick attempt to include all the source code failed :( Feel free to revert my change

@brentp brentp closed this Dec 10, 2023
@brentp brentp deleted the build branch December 10, 2023 08:48
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2 participants