Hello all,
I also get an error after installing an amplicon 2025.4 environment, installing q2-boots, and running qiime info
. I have an M-series Mac and use the rosetta & osx-64 subdir approach (only way to install on ARM Macs as of now). The full traceback is below.
Traceback (most recent call last):
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2cli/util.py", line 275, in get_plugin_manager
return qiime2.sdk.PluginManager.reuse_existing()
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/qiime2/sdk/plugin_manager.py", line 58, in reuse_existing
raise UninitializedPluginManagerError
qiime2.sdk.plugin_manager.UninitializedPluginManagerError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/bin/qiime", line 11, in <module>
sys.exit(qiime())
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/click/core.py", line 1161, in __call__
return self.main(*args, **kwargs)
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/click/core.py", line 1082, in main
rv = self.invoke(ctx)
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/click/core.py", line 1697, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/click/core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/click/core.py", line 788, in invoke
return __callback(*args, **kwargs)
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2cli/builtin/info.py", line 51, in info
import q2cli.core.cache
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2cli/core/cache.py", line 276, in <module>
CACHE = DeploymentCache()
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2cli/core/cache.py", line 61, in __init__
self._state = self._get_cached_state(refresh=refresh)
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2cli/core/cache.py", line 196, in _cache_current_state
state = self._get_current_state()
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2cli/core/cache.py", line 244, in _get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2cli/util.py", line 287, in get_plugin_manager
return qiime2.sdk.PluginManager()
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/qiime2/sdk/plugin_manager.py", line 67, in __new__
self._init(add_plugins=add_plugins)
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
plugin = entry_point.load()
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/importlib/metadata/__init__.py", line 171, in load
module = import_module(match.group('module'))
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_boots/__init__.py", line 13, in <module>
from ._beta import beta, beta_collection, beta_average
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/q2_boots/_beta.py", line 14, in <module>
from hdmedians import medoid
File "/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/hdmedians/__init__.py", line 6, in <module>
from .geomedian import geomedian, nangeomedian
ImportError: dlopen(/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/hdmedians/geomedian.cpython-310-darwin.so, 0x0002): tried: '/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/hdmedians/geomedian.cpython-310-darwin.so' (duplicate LC_RPATH '/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib'), '/System/Volumes/Preboot/Cryptexes/OS/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/hdmedians/geomedian.cpython-310-darwin.so' (no such file), '/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib/python3.10/site-packages/hdmedians/geomedian.cpython-310-darwin.so' (duplicate LC_RPATH '/opt/miniconda3/envs/qiime2-amplicon-2025.4/lib')