Dear all,
After successfully installing qiime2-amplicon-2025.7 by creating a new conda environment on Ubuntu 22.04, I could not even activate the environment. When I run the command conda activate qiime2-amplicon-2025.7, it takes so much time, and then the terminal closes without any message. Would you please help?
Marwa
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/unifrac/init.py:9: UserWarning: pkg_resources is deprecated as an API. See Package Discovery and Resource Access using pkg_resources - setuptools 80.9.0 documentation . The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
Warning: namespace ‘dada2’ is not available and has been replaced
by .GlobalEnv when processing object ‘q_plot10’
Warning: namespace ‘amplicon’ is not available and has been replaced
by .GlobalEnv when processing object ‘amplicon_pkg_alpha_plot’
Warning: namespace ‘phyloseq’ is not available and has been replaced
by .GlobalEnv when processing object ‘ptaxa’
R[write to console]: Error: package or namespace load failed for ‘phyloseq’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/marwa/R/x86_64-pc-linux-gnu-library/4.2/stringi/libs/stringi.so':
/home/marwa/R/x86_64-pc-linux-gnu-library/4.2/stringi/libs/stringi.so: undefined symbol: Rf_charIsASCII
R[write to console]: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/marwa/R/x86_64-pc-linux-gnu-library/4.2/stringi/libs/stringi.so':
/home/marwa/R/x86_64-pc-linux-gnu-library/4.2/stringi/libs/stringi.so: undefined symbol: Rf_charIsASCII
Traceback (most recent call last):
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2cli/util.py", line 275, in get_plugin_manager
return qiime2.sdk.PluginManager.reuse_existing()
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/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 "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/bin/qiime", line 11, in
sys.exit(qiime())
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/click/core.py", line 1161, in call
return self.main(*args, **kwargs)
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/click/core.py", line 1082, in main
rv = self.invoke(ctx)
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/click/core.py", line 1697, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/click/core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/click/core.py", line 788, in invoke
return __callback(*args, **kwargs)
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2cli/builtin/info.py", line 51, in info
import q2cli.core.cache
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2cli/core/cache.py", line 276, in
CACHE = DeploymentCache()
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2cli/core/cache.py", line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2cli/core/cache.py", line 196, in _cache_current_state
state = self._get_current_state()
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2cli/core/cache.py", line 244, in _get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2cli/util.py", line 287, in get_plugin_manager
return qiime2.sdk.PluginManager()
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/qiime2/sdk/plugin_manager.py", line 67, in new
self._init(add_plugins=add_plugins)
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
plugin = entry_point.load()
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/importlib/metadata/init.py", line 171, in load
module = import_module(match.group('module'))
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2_composition/init.py", line 18, in
from ._ancombc2 import ancombc2, ancombc2_visualizer
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2_composition/_ancombc2.py", line 34, in
r_phyloseq = importr('phyloseq')
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/rpy2/robjects/packages.py", line 486, in importr
env = _get_namespace(name)
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/rpy2/rinterface_lib/conversion.py", line 45, in _
cdata = function(*args, **kwargs)
File "/home/marwa/miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/rpy2/rinterface.py", line 817, in call
raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/marwa/R/x86_64-pc-linux-gnu-library/4.2/stringi/libs/stringi.so':
/home/marwa/R/x86_64-pc-linux-gnu-library/4.2/stringi/libs/stringi.so: undefined symbol: Rf_charIsASCII
Hello!
I couldn’t find any information on this error, so I assume that the installation process failed.
Could you try to remove the environment and then install it from scratch?
conda remove -n qiime2-amplicon-2025.7 --all
conda clean --all
Then, reinstall it using the same command.
Best,
Thanks very much for your help