Mamba broken after updating ssl. ImportError: cannot dynamically load position-independent executable
1
vote
0
answers
121
views
I work on a linux server that is running Ubuntu. I have been using miniforge to manage environments with packages for specific tasks. Previously, I was using a global install of anaconda in but removed it from my path (and .bashrc) and deleted my environments associated with it before doing my own install of miniforge.
I installed a package using mamba (
mamba install -c conda-forge -c bioconda r-soupx
) and it updated openssl from 3.2.1 to 3.3.1. The install ran fine, but when loading R to run the package I got an error for a previously working package.
Error: package or namespace load failed for ‘Signac’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/welison/.conda/envs/mamba/envs/seurat5.0_decontx/lib/R/library/Rsamtools/libs/Rsamtools.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)
In a new terminal I activated the environment and ran openssl help
based on reading a github help page and poking around. It ran fine. I started poking around directories and tried running openssl help
from the directory containing the openssl referenced by the environment, and this gave the following error:
openssl: error while loading shared libraries: libssl.so.3: cannot dynamically load position-independent executable
Clearing hash
didn't work, but running openssl help using a path to the global openssl did. I decided to try rolling back the install and ran conda list --revisions
but hit this error:
Traceback (most recent call last):
File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/common/serialize.py", line 12, in
import ruamel.yaml as yaml
File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/ruamel/yaml/__init__.py", line 56, in
from ruamel.yaml.main import * # NOQA
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/ruamel/yaml/main.py", line 17, in
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
from ruamel.yaml.constructor import (
File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/ruamel/yaml/constructor.py", line 4, in
import base64
File "/home/welison/.conda/envs/mamba/lib/python3.11/base64.py", line 11, in
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
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
from ..common.configuration import (
File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/conda/common/configuration.py", line 50, in
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
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
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
import requests
File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/requests/__init__.py", line 43, in
import urllib3
File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/urllib3/__init__.py", line 13, in
from . import exceptions
File "/home/welison/.conda/envs/mamba/lib/python3.11/site-packages/urllib3/exceptions.py", line 7, in
from http.client import IncompleteRead as httplib_IncompleteRead
File "/home/welison/.conda/envs/mamba/lib/python3.11/http/client.py", line 71, in
import email.parser
File "/home/welison/.conda/envs/mamba/lib/python3.11/email/parser.py", line 12, in
from email.feedparser import FeedParser, BytesFeedParser
File "/home/welison/.conda/envs/mamba/lib/python3.11/email/feedparser.py", line 27, in
from email._policybase import compat32
File "/home/welison/.conda/envs/mamba/lib/python3.11/email/_policybase.py", line 7, in
from email import header
File "/home/welison/.conda/envs/mamba/lib/python3.11/email/header.py", line 14, in
import binascii
ImportError: libz.so.1: cannot dynamically load position-independent executable
Every mamba or conda command leads to an error like this, including activating and deactivating environments and search. This is a new problem for me, but a few other users on this server had a similar issue a month back and never managed to resolve it.
Asked by Weston Elison
(11 rep)
Jun 11, 2024, 07:56 PM
Last activity: Jun 11, 2024, 07:56 PM
Last activity: Jun 11, 2024, 07:56 PM