Trouble installing latest qiime (2026.1)

Technical Support
1

hi qiime team,

after reading through the related topics, I haven’t come across my problem yet unfortunatley.. I’m trying to update to the latest qiime2 version (2026.1) and after running conda update conda I run the command from the install page and get these errors (this is a small section of it):

ClobberError: The package 'conda-forge/noarch::parsl-2024.4.15-pyhd8ed1ab_0' cannot be installed due to a
path collision for 'lib/python3.10/site-packages/parsl/pycache/version.cpython-310.pyc'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.

ClobberError: The package 'bioconda/noarch::rnanorm-2.1.0-pyhdfd78af_0' cannot be installed due to a
path collision for 'lib/python3.10/site-packages/rnanorm/pycache/init.cpython-310.pyc'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.

ClobberError: The package 'bioconda/noarch::rnanorm-2.1.0-pyhdfd78af_0' cannot be installed due to a
path collision for 'lib/python3.10/site-packages/rnanorm/pycache/annotation.cpython-310.pyc'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.

ClobberError: The package 'bioconda/noarch::rnanorm-2.1.0-pyhdfd78af_0' cannot be installed due to a
path collision for 'lib/python3.10/site-packages/rnanorm/methods/pycache/init.cpython-310.pyc'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.

ClobberError: The package 'bioconda/noarch::rnanorm-2.1.0-pyhdfd78af_0' cannot be installed due to a
path collision for 'lib/python3.10/site-packages/rnanorm/methods/pycache/between_sample.cpython-310.pyc'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.

ClobberError: The package 'bioconda/noarch::rnanorm-2.1.0-pyhdfd78af_0' cannot be installed due to a
path collision for 'lib/python3.10/site-packages/rnanorm/methods/pycache/utils.cpython-310.pyc'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.

ClobberError: The package 'bioconda/noarch::rnanorm-2.1.0-pyhdfd78af_0' cannot be installed due to a
path collision for 'lib/python3.10/site-packages/rnanorm/methods/pycache/within_sample.cpython-310.pyc'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.

ClobberError: The package 'bioconda/noarch::rnanorm-2.1.0-pyhdfd78af_0' cannot be installed due to a
path collision for 'lib/python3.10/site-packages/rnanorm/pycache/typing.cpython-310.pyc'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.

done
Executing transaction: done
ERROR conda.core.link:_execute(1033): An error occurred while installing package 'conda-forge::openmpi-4.1.6-hc5af2df_101'.
Rolling back transaction: done

LinkError: post-link script failed for package conda-forge::openmpi-4.1.6-hc5af2df_101
location of failed script: /home/WUR/polli003/miniconda3/envs/qiime2-amplicon-2026.1/bin/.openmpi-post-link.sh
==> script messages <==

==> script output <==
stdout:
stderr:
return code: 1

()

And on and on and on.. not sure what is going on, something to do with the R user library?

Let me know if more information is required.

Regards

Marcel

2

Hi @marcelpolling,

Given the error you are observing, I am going to guess that you are running conda version ~26.1.1 or similar. Some information and instructions are outlined here.

1 Like
4

Hi @SoilRotifer!

and thanks for the very quick reply :slight_smile: Unfortunately, I did already try this, but still got these strange ClobberErrors..

regards

Marcel

5

Hey @marcelpolling,

This is strange; R wasn't my first guess on what could be going wrong here but since you brought it up, do you have R installed on your native machine (outside of any conda environments)?

6

I assume, you also run:

conda clean --all

after it?

7

Hi @timanix , I tried the above suggestions and got it installed without the issues! .. only thing is that if I run it I keep getting errors that I have with no other qiime2 dist ever before: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
R callback write-console: Error: package or namespace load failed for ‘phyloseq’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/WUR/polli003/R/library/ade4/libs/ade4.so':
libflexiblas.so.3: cannot open shared object file: No such file or directory

R callback write-console: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/WUR/polli003/R/library/ade4/libs/ade4.so':
libflexiblas.so.3: cannot open shared object file: No such file or directory

Traceback (most recent call last):
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2cli/util.py", line 277, in get_plugin_manager
return qiime2.sdk.PluginManager.reuse_existing()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/rachis/sdk/plugin_manager.py", line 64, in reuse_existing
raise UninitializedPluginManagerError
rachis.sdk.plugin_manager.UninitializedPluginManagerError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/bin/qiime", line 11, in
sys.exit(qiime())
^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/click/core.py", line 1161, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/click/core.py", line 1081, in main
with self.make_context(prog_name, args, **extra) as ctx:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/click/core.py", line 949, in make_context
self.parse_args(ctx, args)
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/click/core.py", line 1653, in parse_args
rest = super().parse_args(ctx, args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/click/core.py", line 1417, in parse_args
value, args = param.handle_parse_result(ctx, opts, args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/click/core.py", line 2403, in handle_parse_result
value = self.process_value(ctx, value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/click/core.py", line 2365, in process_value
value = self.callback(ctx, self, value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/click/decorators.py", line 550, in show_help
echo(ctx.get_help(), color=ctx.color)
^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/click/core.py", line 711, in get_help
return self.command.get_help(self)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/click/core.py", line 1334, in get_help
self.format_help(ctx, formatter)
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/click/core.py", line 1367, in format_help
self.format_options(ctx, formatter)
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2cli/click/command.py", line 157, in format_options
for subcommand in self.list_commands(ctx):
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2cli/commands.py", line 92, in list_commands
plugins = sorted(self._plugin_lookup)
^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
import q2cli.core.cache
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2cli/core/cache.py", line 276, in
CACHE = DeploymentCache()
^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2cli/core/cache.py", line 61, in init
self._state = self._get_cached_state(refresh=refresh)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2cli/core/cache.py", line 196, in _cache_current_state
state = self._get_current_state()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2cli/core/cache.py", line 244, in _get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2cli/util.py", line 289, in get_plugin_manager
return qiime2.sdk.PluginManager()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/rachis/sdk/plugin_manager.py", line 73, in new
self._init(add_plugins=add_plugins)
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/rachis/sdk/plugin_manager.py", line 111, in _init
plugin = entry_point.load()
^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/importlib/metadata/init.py", line 205, in load
module = import_module(match.group('module'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/importlib/init.py", line 90, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2_composition/init.py", line 18, in
from ._ancombc2 import ancombc2, ancombc2_visualizer
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/q2_composition/_ancombc2.py", line 34, in
r_phyloseq = importr('phyloseq')
^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/rpy2/robjects/packages.py", line 486, in importr
env = _get_namespace(name)
^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/rpy2/rinterface_lib/conversion.py", line 46, in _
cdata = function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/WUR/polli003/miniconda3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/rpy2/rinterface/init.py", line 926, 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/WUR/polli003/R/library/ade4/libs/ade4.so':
libflexiblas.so.3: cannot open shared object file: No such file or directory

8

At least it worked for installation... :upside_down_face:

I would try:

  1. Delete it again
  2. run "conda clean --all"
  3. Install the latest version if qiime2 again
  4. If not working, clean conda again and go for the previous version of qiime2 until it works...

As an option, if you don't have much in your conda environment, I would try reinstalling conda (for example, miniforge3).

Best,

9

Been working on this a bit more and finally found a solution: it was an R error apparently.. after telling Conda to ignore my home R library it worked echo "R_LIBS_USER=" > ~/.Renviron. Thanks for all the help!!

1 Like