QIIme caching error

[Charles_Hauser]

Hi

Installed qiime2 on a unix server running Red Hat Enterprise Linux Server release 7.9 (Maipo)

We are getting the following error when qiime attempts to cache:

Suggestions?

Charles

_______

(qiime2-amplicon-2025.7) csbinf03:~ => qiime info

QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.

…../miniconda3/envs/qiime2-amplicon-2025.7/lib/python3.10/site-packages/q2_demux/_summarize/_visualizer.py:11: 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.

R[write to console]: Error: package or namespace load failed for ‘ANCOMBC’ in dyn.load(file, DLLpath = DLLpath, ...):

unable to load shared object '/home/charlesh@seu.stedwards.edu/miniconda3/envs/qiime2-amplicon-2025.7/lib/R/library/gsl/libs/gsl.so':

libgsl.so.25: cannot open shared object file: No such file or directory

R[write to console]: Error in dyn.load(file, DLLpath = DLLpath, ...) :

unable to load shared object '/home/charlesh@seu.stedwards.edu/miniconda3/envs/qiime2-amplicon-2025.7/lib/R/library/gsl/libs/gsl.so':

libgsl.so.25: cannot open shared object file: No such file or directory

Traceback (most recent call last):

File "/home/charlesh@seu.stedwards.edu/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/charlesh@seu.stedwards.edu/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:

[ebolyen (Evan Bolyen)]

So it seems that an R dependency is missing... it usually comes along for the ride with the environment-file without issue, so I haven't seen this exact package being an issue before.

Would you mind confirming the install instructions you used?

---

We might try the old "uninstall and reinstall" and hope that magically fixes things.
Right after you remove the env

conda env remove -n qiime2-amplicon-2025.7

You may want to run:

conda clean --all

which will get rid of any potentially corrupted packages which could still get pulled in when you re-install.

Sorry I don't have a better suggestion (yet)!

[Charles_Hauser]

Evan

Thanks for reply.

Install cmd used was:

1967 conda env create --name qiime2-amplicon-2025.7 --file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2025.7/amplicon/released/qiime2-amplicon-ubuntu-latest-conda.yml

1969 conda activate qiime2-amplicon-2025.7

I removed previous install and ran “conda clean –all” - (lots of hanging chads removed) and reinstalled.

Success - problem resolved.:

csbinf03:~ => conda activate qiime2-amplicon-2025.7

(qiime2-amplicon-2025.7) csbinf03:~ =>

Thanks for your help

Charles