Empress install error

Technical Support
1

Having this error after installing empress and running dev refresh-cache. Any help would be greatly appreciated :smiley:

My Stuff:
miniconda3
qiime2-amplicon-2024.10
Apple M1 chip

commands ran:
pip install empress
qiime dev refresh-cache

QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/util.py", line 273, in get_plugin_manager
return qiime2.sdk.PluginManager.reuse_existing()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/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 "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/bin/qiime", line 11, in
sys.exit(qiime())
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/builtin/dev.py", line 33, in refresh_cache
import q2cli.core.cache
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/core/cache.py", line 285, in
CACHE = DeploymentCache()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/core/cache.py", line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/core/cache.py", line 205, in _cache_current_state
state = self._get_current_state()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/core/cache.py", line 253, in _get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/util.py", line 285, in get_plugin_manager
return qiime2.sdk.PluginManager()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/plugin_manager.py", line 67, in new
self._init(add_plugins=add_plugins)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
plugin = entry_point.load()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/pkg_resources/init.py", line 2781, in load
return self.resolve()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/pkg_resources/init.py", line 2787, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/empress/init.py", line 9, in
from empress.core import Empress
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/empress/core.py", line 24, in
from emperor import Emperor
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/emperor/init.py", line 12, in
from emperor.core import Emperor
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/emperor/core.py", line 19, in
from skbio import OrdinationResults
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/init.py", line 11, in
import skbio.io # noqa
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/io/init.py", line 244, in
import_module('skbio.io.format.clustal')
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/io/format/clustal.py", line 148, in
from skbio.alignment import TabularMSA
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/alignment/init.py", line 203, in
from ._tabular_msa import TabularMSA
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/alignment/_tabular_msa.py", line 17, in
from skbio.metadata._mixin import MetadataMixin, PositionalMetadataMixin
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/metadata/init.py", line 27, in
from ._interval import Interval, IntervalMetadata
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/metadata/_interval.py", line 13, in
from ._intersection import IntervalTree
ImportError: dlopen(/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/metadata/_intersection.cpython-310-darwin.so, 0x0002): tried: '/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/metadata/_intersection.cpython-310-darwin.so' (duplicate LC_RPATH '/opt/miniconda3/envs/qiime2-amplicon-2024.10/lib'), '/System/Volumes/Preboot/Cryptexes/OS/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/metadata/_intersection.cpython-310-darwin.so' (no such file), '/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/skbio/metadata/_intersection.cpython-310-darwin.so' (duplicate LC_RPATH '/opt/miniconda3/envs/qiime2-amplicon-2024.10/lib')

4

Hi @Shailey_Heller,

Welcome to the :qiime2: forum!
@colinbrislawn found an issue on github with a workaround that may help you!
with your amplicon environment activated, run:

  1. pip install Cython==0.29.37
  2. pip install iow==1.0.7
  3. pip install empress

Hopefully that works! if not please follow up here :slight_smile:

--Hannah

1 Like
5

Hi @jphagen, Thank you for your help! Still having issues with qiime dev refresh-cache.

commands:
pip install Cython==0.29.37
pip install iow==1.0.7
pip install empress

qiime dev refresh-cache output:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/util.py", line 273, in get_plugin_manager
return qiime2.sdk.PluginManager.reuse_existing()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/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 "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/bin/qiime", line 11, in
sys.exit(qiime())
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/builtin/dev.py", line 33, in refresh_cache
import q2cli.core.cache
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/core/cache.py", line 285, in
CACHE = DeploymentCache()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/core/cache.py", line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/core/cache.py", line 205, in _cache_current_state
state = self._get_current_state()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/core/cache.py", line 253, in _get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/util.py", line 285, in get_plugin_manager
return qiime2.sdk.PluginManager()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/plugin_manager.py", line 67, in new
self._init(add_plugins=add_plugins)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
plugin = entry_point.load()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/pkg_resources/init.py", line 2781, in load
return self.resolve()
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/pkg_resources/init.py", line 2787, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/empress/plugin_setup.py", line 9, in
from ._plot import community_plot, tree_plot
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/empress/_plot.py", line 16, in
from empress._plot_utils import get_bp, save_viz, prepare_pcoa
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/empress/_plot_utils.py", line 13, in
from bp import parse_newick
File "/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/bp/init.py", line 8, in
from ._bp import BP
ImportError: dlopen(/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/bp/_bp.cpython-310-darwin.so, 0x0002): tried: '/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/bp/_bp.cpython-310-darwin.so' (duplicate LC_RPATH '/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib'), '/System/Volumes/Preboot/Cryptexes/OS/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/bp/_bp.cpython-310-darwin.so' (no such file), '/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/bp/_bp.cpython-310-darwin.so' (duplicate LC_RPATH '/Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib')

6

Hi @Shailey_Heller,
Can you please run:

ls /Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/bp/

and post the output here?

This error is indicating that this file is missing from the bp package so I want to check that if it actually is.

--Hannah

1 Like
11

Hi Hanna,

Here is the output:

ls /Users/shaileyheller/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/bp

__init__.py				_conv.cpython-310-darwin.so
__pycache__				_insert.cpython-310-darwin.so
_ba.cpython-310-darwin.so		_io.cpython-310-darwin.so
_binary_tree.cpython-310-darwin.so	_version.py
_bp.cpython-310-darwin.so		BitArray
_cli.py					tests
13

Hi @Shailey_Heller,

This problem you are seeing is seems like it could be a deeper issue. A senior moderator related to this issue has been notified but they are on leave at this time. I am sorry, I wish I had a quicker fix for you!

--Hannah

1 Like
15

Thank you for your help!

1 Like