Solution to issue cannot be found in the documentation.
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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.
Solution to issue cannot be found in 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:I poked around looking at that libssl library (
libssl helpfrom 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 --revisionsgave: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
Environment info