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I investigated a bit, and ran the command there (conda env update --name grenepipe --file envs/grenepipe.yaml) locally on my machine (Ubuntu 20.04.5 LTS), with conda 22.9.0, and got an error as well:
ModuleNotFoundError: No module named '_sysconfigdata_x86_64_conda_cos7_linux_gnu'
Full output
> conda env create --name grenepipe-update-test --file envs/grenepipe.yaml
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/lucas/Software/miniconda/lib/python3.8/argparse.py", line 1800, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/lucas/Software/miniconda/lib/python3.8/argparse.py", line 1988, in _parse_known_args
positionals_end_index = consume_positionals(start_index)
File "/home/lucas/Software/miniconda/lib/python3.8/argparse.py", line 1965, in consume_positionals
take_action(action, args)
File "/home/lucas/Software/miniconda/lib/python3.8/argparse.py", line 1858, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/lucas/Software/miniconda/lib/python3.8/argparse.py", line 2399, in _get_values
self._check_value(action, value[0])
File "/home/lucas/Software/miniconda/lib/python3.8/argparse.py", line 2446, in _check_value
raise ArgumentError(action, msg % args)
argparse.ArgumentError: argument command: invalid choice: 'env' (choose from 'clean', 'compare', 'config', 'create', 'info', 'init', 'install', 'list', 'package', 'remove', 'rename', 'run', 'search', 'uninstall', 'update', 'upgrade', 'notices')
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/lucas/Software/miniconda/lib/python3.8/site-packages/conda/exceptions.py", line 1129, in __call__
return func(*args, **kwargs)
File "/home/lucas/Software/miniconda/lib/python3.8/site-packages/conda/cli/main.py", line 75, in main_subshell
args = p.parse_args(args)
File "/home/lucas/Software/miniconda/lib/python3.8/argparse.py", line 1768, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/lucas/Software/miniconda/lib/python3.8/argparse.py", line 1807, in parse_known_args
self.error(str(err))
File "/home/lucas/Software/miniconda/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 154, in error
executable = find_executable('conda-' + cmd)
File "/home/lucas/Software/miniconda/lib/python3.8/site-packages/conda/cli/find_commands.py", line 25, in find_executable
dir_paths = [join(p, basename(sysconfig.get_path('scripts')))
File "/home/lucas/Software/miniconda/lib/python3.8/site-packages/conda/cli/find_commands.py", line 25, in <listcomp>
dir_paths = [join(p, basename(sysconfig.get_path('scripts')))
File "/home/lucas/Software/miniconda/lib/python3.8/sysconfig.py", line 521, in get_path
return get_paths(scheme, vars, expand)[name]
File "/home/lucas/Software/miniconda/lib/python3.8/sysconfig.py", line 511, in get_paths
return _expand_vars(scheme, vars)
File "/home/lucas/Software/miniconda/lib/python3.8/sysconfig.py", line 172, in _expand_vars
_extend_dict(vars, get_config_vars())
File "/home/lucas/Software/miniconda/lib/python3.8/sysconfig.py", line 559, in get_config_vars
_init_posix(_CONFIG_VARS)
File "/home/lucas/Software/miniconda/lib/python3.8/sysconfig.py", line 430, in _init_posix
_temp = __import__(name, globals(), locals(), ['build_time_vars'], 0)
ModuleNotFoundError: No module named '_sysconfigdata_x86_64_conda_cos7_linux_gnu'
`$ /home/lucas/Software/miniconda/bin/conda env create --name grenepipe-update-test --file envs/grenepipe.yaml`
environment variables:
CIO_TEST=<not set>
CMAKE_PREFIX_PATH=/home/lucas/Software/miniconda:/home/lucas/Software/miniconda/x86_64-c
onda-linux-gnu/sysroot/usr
CONDA_BUILD_SYSROOT=/home/lucas/Software/miniconda/x86_64-conda-linux-gnu/sysroot
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/lucas/Software/miniconda/bin/conda
CONDA_PREFIX=/home/lucas/Software/miniconda
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/lucas/Software/miniconda/bin/python
CONDA_ROOT=/home/lucas/Software/miniconda
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
PATH=/home/lucas/Software/miniconda/bin:/home/lucas/Software/miniconda/cond
abin:/home/lucas/.cargo/bin:/home/lucas/.local/bin:/usr/local/sbin:/us
r/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:
/snap/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
TERMINATOR_DBUS_PATH=/net/tenshu/Terminator2
WINDOWPATH=2
active environment : base
active env location : /home/lucas/Software/miniconda
shell level : 1
user config file : /home/lucas/.condarc
populated config files :
conda version : 22.9.0
conda-build version : not installed
python version : 3.8.5.final.0
virtual packages : __linux=5.15.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/lucas/Software/miniconda (writable)
conda av data dir : /home/lucas/Software/miniconda/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/lucas/Software/miniconda/pkgs
/home/lucas/.conda/pkgs
envs directories : /home/lucas/Software/miniconda/envs
/home/lucas/.conda/envs
platform : linux-64
user-agent : conda/22.9.0 requests/2.28.1 CPython/3.8.5 Linux/5.15.0-52-generic ubuntu/20.04.5 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]: y
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$ conda config --set report_errors true
That looks more like an issue with conda than with setup-miniconda. The whole thing works nicely once I add mamba-version: "*" to the GitHub Action with: clause. This confirms that this issue is with conda.
However, I'm still opening the issue here in order to suggest that the output of the Action includes the full conda error output, to make debugging easier.
Cheers
Lucas
The text was updated successfully, but these errors were encountered:
Hi there,
this error is similar to #116, but yet seems to be a different error, or caused by a different problem.
My GitHub Action step looks like this:
This results in the following error:
(that's the part that seems similar to #116).
I investigated a bit, and ran the command there (
conda env update --name grenepipe --file envs/grenepipe.yaml
) locally on my machine (Ubuntu 20.04.5 LTS), with conda 22.9.0, and got an error as well:Full output
That looks more like an issue with conda than with setup-miniconda. The whole thing works nicely once I add
mamba-version: "*"
to the GitHub Actionwith:
clause. This confirms that this issue is with conda.However, I'm still opening the issue here in order to suggest that the output of the Action includes the full conda error output, to make debugging easier.
Cheers
Lucas
The text was updated successfully, but these errors were encountered: