adds with_conformer option to copy_mol_subset #27
Annotations
1 error and 4 warnings
Run conda-incubator/setup-miniconda@v2
The process '/usr/share/miniconda3/condabin/mamba' failed with exit code 1
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Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Run conda-incubator/setup-miniconda@v2
Mamba support is still experimental and can result in differently solved environments!
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Run conda-incubator/setup-miniconda@v2
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/usr/share/miniconda3/lib/python3.10/site-packages/conda/exception_handler.py", line 17, in __call__
return func(*args, **kwargs)
File "/usr/share/miniconda3/lib/python3.10/site-packages/conda_env/cli/main.py", line 56, in do_call
exit_code = getattr(module, func_name)(arguments, parser)
File "/usr/share/miniconda3/lib/python3.10/site-packages/conda/notices/core.py", line 124, in wrapper
return func(*args, **kwargs)
File "/usr/share/miniconda3/lib/python3.10/site-packages/conda_env/cli/main_update.py", line 143, in execute
result[installer_type] = installer.install(prefix, specs, args, env)
File "/usr/share/miniconda3/lib/python3.10/site-packages/mamba/mamba_env.py", line 54, in mamba_install
index = load_channels(pool, channel_urls, repos, prepend=False)
File "/usr/share/miniconda3/lib/python3.10/site-packages/mamba/utils.py", line 126, in load_channels
index = get_index(
File "/usr/share/miniconda3/lib/python3.10/site-packages/mamba/utils.py", line 107, in get_index
is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)
RuntimeError: Download error (28) Timeout was reached [https://conda.anaconda.org/jaimergp/label/unsupported-cudatoolkit-shim/noarch/repodata.json.zst]
Operation too slow. Less than 30 bytes/sec transferred the last 60 seconds
`$ /usr/share/miniconda3/condabin/mamba update --name pdbinf --file /home/runner/work/pdbinf/pdbinf/setup-miniconda-patched-ci_env.yml`
environment variables:
CIO_TEST=<not set>
CONDA=/usr/share/miniconda3
CONDA_AUTO_UPDATE_CONDA=false
CONDA_PKGS_DIR=/home/runner/conda_pkgs_dir
CONDA_ROOT=/usr/share/miniconda3
CURL_CA_BUNDLE=<not set>
DEPLOYMENT_BASEPATH=/opt/runner
GITHUB_EVENT_PATH=/home/runner/work/_temp/_github_workflow/event.json
GITHUB_PATH=/home/runner/work/_temp/_runner_file_commands/add_path_4fb0187e-1b2e-
4048-8e61-062f6405ee3e
LD_PRELOAD=<not set>
PATH=/usr/share/miniconda3/condabin:/snap/bin:/home/runner/.local/bin:/opt/
pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/
bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/
usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/game
s:/snap/bin
REQUESTS_CA_BUNDLE=<not set>
SELENIUM_JAR_PATH=/usr/share/java/selenium-server.jar
SSL_CERT_FILE=<not set>
SWIFT_PATH=/usr/share/swift/usr/bin
active environment : None
user config file : /home/runner/.condarc
populated config files : /usr/share/miniconda3/.condarc
/home/runner/.condarc
conda version : 23.11.0
conda-build version : not installed
python version : 3.10.13.final.0
solver : libmamba (default)
virtual packages : __archspec=1=zen2
__conda=23.11.0=0
__glibc=2.35=0
__linux=6.5.0=0
__unix=0=0
base environment : /usr/share/miniconda3 (writable)
conda av data dir : /usr/share/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/jaimergp/label/unsupported-cudatoolkit-shim/linux-64
https://conda.anaconda.org/jaimergp/label/unsupported-cudatoolkit-shim/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
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