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Error while executing scout after a fresh conda installation - ARM processor #4405

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northwestwitch opened this issue Feb 6, 2024 · 0 comments

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@northwestwitch
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northwestwitch commented Feb 6, 2024

(py39) chiararasi@n190-p146 scout % scout --demo serve
Traceback (most recent call last):
  File "/Users/chiararasi/miniconda3/envs/py39/bin/scout", line 33, in <module>
    sys.exit(load_entry_point('scout-browser', 'console_scripts', 'scout')())
  File "/Users/chiararasi/miniconda3/envs/py39/bin/scout", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/Users/chiararasi/miniconda3/envs/py39/lib/python3.9/importlib/metadata.py", line 86, in load
    module = import_module(match.group('module'))
  File "/Users/chiararasi/miniconda3/envs/py39/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/Users/chiararasi/Documents/work/GITs/scout/scout/commands/__init__.py", line 1, in <module>
    from .base import cli
  File "/Users/chiararasi/Documents/work/GITs/scout/scout/commands/base.py", line 12, in <module>
    from scout.commands.convert import convert
  File "/Users/chiararasi/Documents/work/GITs/scout/scout/commands/convert.py", line 8, in <module>
    from scout.server.extensions import store
  File "/Users/chiararasi/Documents/work/GITs/scout/scout/server/extensions/__init__.py", line 8, in <module>
    from scout.adapter import MongoAdapter
  File "/Users/chiararasi/Documents/work/GITs/scout/scout/adapter/__init__.py", line 1, in <module>
    from scout.adapter.mongo.base import MongoAdapter
  File "/Users/chiararasi/Documents/work/GITs/scout/scout/adapter/mongo/__init__.py", line 1, in <module>
    from .base import MongoAdapter
  File "/Users/chiararasi/Documents/work/GITs/scout/scout/adapter/mongo/base.py", line 35, in <module>
    from .case import CaseHandler
  File "/Users/chiararasi/Documents/work/GITs/scout/scout/adapter/mongo/case.py", line 15, in <module>
    from scout.parse.variant.ids import parse_document_id
  File "/Users/chiararasi/Documents/work/GITs/scout/scout/parse/variant/__init__.py", line 1, in <module>
    from .variant import parse_variant
  File "/Users/chiararasi/Documents/work/GITs/scout/scout/parse/variant/variant.py", line 4, in <module>
    from cyvcf2 import Variant
  File "/Users/chiararasi/miniconda3/envs/py39/lib/python3.9/site-packages/cyvcf2/__init__.py", line 1, in <module>
    from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
ImportError: dlopen(/Users/chiararasi/miniconda3/envs/py39/lib/python3.9/site-packages/cyvcf2/cyvcf2.cpython-39-darwin.so, 0x0002): symbol not found in flat namespace '_bcf_float_missing'

See brentp/cyvcf2#297

If this happens uninstall cyvcf2 from the environment and install the latest with wheels

In my case this worked:
pip install cyvcf2==v0.30.25

@northwestwitch northwestwitch changed the title Error while installing scout with ARM processor Error while executing scout after a fresh conda installation - ARM processor Feb 6, 2024
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