I went back to my original error which is similar to what is here, but the solution did not work for me.
I removed the environment, ran conda clean --all, started from scratch to reproduce the first error (repeated below).
I then tried to update scikit-learn and received:
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. umap-learn 0.5.3 requires scikit-learn>=0.22, but you have scikit-learn 0.20.3 which is incompatible.
When I check the glibc version with ldd --version I see
ldd (Ubuntu EGLIBC 2.19-0ubuntu6.14) 2.19 Copyright (C) 2014 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Written by Roland McGrath and Ulrich Drepper.
I'm pretty lost.
first error:
qiime2.sdk.plugin_manager.UninitializedPluginManagerError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/bin/qiime", line 11, in
sys.exit(qiime())
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1054, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 920, in make_context
self.parse_args(ctx, args)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1610, in parse_args
echo(ctx.get_help(), color=ctx.color)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 699, in get_help
return self.command.get_help(self)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1298, in get_help
self.format_help(ctx, formatter)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1331, in format_help
self.format_options(ctx, formatter)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/click/command.py", line 157, in format_options
for subcommand in self.list_commands(ctx):
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/commands.py", line 92, in list_commands
plugins = sorted(self._plugin_lookup)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
import q2cli.core.cache
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 285, in
CACHE = DeploymentCache()
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 205, in _cache_current_state
state = self._get_current_state()
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 253, in _get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/util.py", line 278, in get_plugin_manager
return qiime2.sdk.PluginManager()
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 67, in new
self._init(add_plugins=add_plugins)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
plugin = entry_point.load()
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/pkg_resources/init.py", line 2517, in load
return self.resolve()
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/pkg_resources/init.py", line 2523, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_alignment/init.py", line 9, in
from ._mafft import mafft, mafft_add
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 11, in
import skbio
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/init.py", line 19, in
import skbio.diversity # noqa
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/diversity/init.py", line 402, in
from ._driver import (alpha_diversity, beta_diversity, partial_beta_diversity,
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/diversity/_driver.py", line 13, in
import sklearn.metrics
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/sklearn/init.py", line 83, in
from .utils._show_versions import show_versions
File "/home/guestuser/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/sklearn/utils/_show_versions.py", line 12, in
from ._openmp_helpers import _openmp_parallelism_enabled
ImportError: dlopen: cannot load any more object with static TLS`