ImportError with dynamic libraries

[westonelison]

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Today I installed a package in my environment mamba install -c conda-forge -c bioconda r-soupx, which worked fine. This upgraded openssl from 3.2 to 3.3. When running R from this environment one of the previous packages was unable to load with this error:

Error: package or namespace load failed for ‘hdf5r’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/welison/.conda/envs/mamba/envs/seurat5.0_decontx/lib/R/library/hdf5r/libs/hdf5r.so':
  /home/welison/.conda/envs/decontX_reticulate/lib/python3.10/lib-dynload/../../libcrypto.so.3: version `OPENSSL_3.3.0' not found (required by /home/welison/.conda/envs/mamba/envs/seurat5.0_decontx/lib/././libssl.so.3)

I poked around looking at that libssl library (libssl help from my working directory which worked, then moved to the directory containing the library and it failed, openssl: error while loading shared libraries: libssl.so.3: cannot dynamic). After this I decided to go back one revision on this environment. conda list --revisions gave:

Traceback (most recent call last):
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/common/serialize.py", line 12, in <module>
    import ruamel.yaml as yaml
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/ruamel/yaml/__init__.py", line 56, in <module>
    from ruamel.yaml.main import *  # NOQA
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/ruamel/yaml/main.py", line 17, in <module>
    from ruamel.yaml.loader import BaseLoader, SafeLoader, Loader, RoundTripLoader  # NOQA
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/ruamel/yaml/loader.py", line 7, in <module>
    from ruamel.yaml.constructor import (
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/ruamel/yaml/constructor.py", line 4, in <module>
    import base64
  File "/home/welison/.conda/envs/mamba/lib/python3.11/base64.py", line 11, in <module>
    import binascii
ImportError: libz.so.1: cannot dynamically load position-independent executable

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/common/serialize.py", line 15, in <module>
    import ruamel_yaml as yaml
ModuleNotFoundError: No module named 'ruamel_yaml'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/exception_handler.py", line 17, in __call__
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/cli/main.py", line 36, in main_subshell
    from ..base.context import context
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/base/context.py", line 35, in <module>
    from ..common.configuration import (
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/common/configuration.py", line 50, in <module>
    from .serialize import yaml_round_trip_load
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/common/serialize.py", line 17, in <module>
    raise ImportError(
ImportError: No yaml library available. To proceed, conda install ruamel.yaml

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/welison/.conda/envs/mamba/bin/conda", line 13, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/cli/main.py", line 109, in main
    return conda_exception_handler(main, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/exception_handler.py", line 389, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/exception_handler.py", line 20, in __call__
    return self.handle_exception(exc_val, exc_tb)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/exception_handler.py", line 52, in handle_exception
    from .exceptions import (
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/exceptions.py", line 15, in <module>
    import requests
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/requests/__init__.py", line 43, in <module>
    import urllib3
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/urllib3/__init__.py", line 13, in <module>
    from . import exceptions
  File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/urllib3/exceptions.py", line 7, in <module>
    from http.client import IncompleteRead as httplib_IncompleteRead
  File "/home/welison/.conda/envs/mamba/lib/python3.11/http/client.py", line 71, in <module>
    import email.parser
  File "/home/welison/.conda/envs/mamba/lib/python3.11/email/parser.py", line 12, in <module>
    from email.feedparser import FeedParser, BytesFeedParser
  File "/home/welison/.conda/envs/mamba/lib/python3.11/email/feedparser.py", line 27, in <module>
    from email._policybase import compat32
  File "/home/welison/.conda/envs/mamba/lib/python3.11/email/_policybase.py", line 7, in <module>
    from email import header
  File "/home/welison/.conda/envs/mamba/lib/python3.11/email/header.py", line 14, in <module>
    import binascii
ImportError: libz.so.1: cannot dynamically load position-independent executable

Now any conda or mamba command gives a similar error (activate, deactivate, init, search, clean). A few other users of this server have had similar issues and had to completely uninstall and reinstall mamba, but with only partial success. My googling hasn't been very helpful, but I will keep looking from my end.

Oh, and potentially relevant: There is a global anaconda3 install, which I used a few years back but removed from my paths and bashrc and now I only reference miniforge. That global anaconda3 is still there and referenced by other users.

Installed packages

Can't run

Environment info

Can't run

[jaimergp]

This type of path (/home/welison/.conda/envs/mamba/envs/seurat5.0_decontx/lib/././libssl.so.3) suggests you have installed mamba inside Miniforge, as a new environment which has been marked as base, and now you have more environmetns there (see the two envs/ components).

Double check how your ~/.bashrc looks like because you might have a few initialization blocks there.