add further R scripts, moved #139
Annotations
1 error and 5 warnings
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Run conda-incubator/setup-miniconda@v2
The process '/usr/share/miniconda/condabin/mamba' failed with exit code 1
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Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@v1. Please update your workflow to use the latest version of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-09-16-notice-of-upcoming-deprecations-and-changes-in-github-actions-services/
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ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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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
info libmamba ****************** Backtrace Start ******************
debug libmamba Loading configuration
trace libmamba Compute configurable 'create_base'
trace libmamba Compute configurable 'no_env'
trace libmamba Compute configurable 'no_rc'
trace libmamba Compute configurable 'rc_files'
trace libmamba Compute configurable 'root_prefix'
warning libmamba You have not set the root prefix environment variable.
To permanently modify the root prefix location, either:
- set the 'MAMBA_ROOT_PREFIX' environment variable
- use the '-r,--root-prefix' CLI option
- use 'mamba shell init ...' to initialize your shell
(then restart or source the contents of the shell init script)
Continuing with default value: "/usr/share/miniconda"
trace libmamba Get RC files configuration from locations up to HomeDir
trace libmamba Configuration not found at '/home/runner/.mambarc'
trace libmamba Configuration not found at '/home/runner/.mamba/mambarc.d'
trace libmamba Configuration not found at '/home/runner/.mamba/mambarc'
trace libmamba Configuration not found at '/home/runner/.mamba/.mambarc'
trace libmamba Configuration not found at '/home/runner/.config/mamba/mambarc.d'
trace libmamba Configuration not found at '/home/runner/.config/mamba/mambarc'
trace libmamba Configuration not found at '/home/runner/.config/mamba/.mambarc'
trace libmamba Configuration found at '/home/runner/.condarc'
trace libmamba Configuration not found at '/home/runner/.conda/condarc.d'
trace libmamba Configuration not found at '/home/runner/.conda/condarc'
trace libmamba Configuration not found at '/home/runner/.conda/.condarc'
trace libmamba Configuration not found at '/home/runner/.config/conda/condarc.d'
trace libmamba Configuration not found at '/home/runner/.config/conda/condarc'
trace libmamba Configuration not found at '/home/runner/.config/conda/.condarc'
trace libmamba Configuration not found at '/usr/share/miniconda/.mambarc'
trace libmamba Configuration not found at '/usr/share/miniconda/condarc.d'
trace libmamba Configuration not found at '/usr/share/miniconda/condarc'
trace libmamba Configuration found at '/usr/share/miniconda/.condarc'
trace libmamba Configuration not found at '/var/lib/conda/.mambarc'
trace libmamba Configuration not found at '/var/lib/conda/condarc.d/'
trace libmamba Configuration not found at '/var/lib/conda/condarc'
trace libmamba Configuration not found at '/var/lib/conda/.condarc'
trace libmamba Configuration not found at '/etc/conda/.mambarc'
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Run conda-incubator/setup-miniconda@v2
trace libmamba Configuration not found at '/etc/conda/condarc.d/'
trace libmamba Configuration not found at '/etc/conda/condarc'
trace libmamba Configuration not found at '/etc/conda/.condarc'
trace libmamba Update configurable 'no_env'
trace libmamba Compute configurable 'envs_dirs'
trace libmamba Compute configurable 'file_specs'
debug libmamba No env 'name' specified in YAML spec file '/home/runner/work/cgat-flow/cgat-flow/conda/environments/setup-miniconda-patched-cgat-flow-pipelines.yml'
trace libmamba Compute configurable 'spec_file_env_name'
trace libmamba Compute configurable 'env_name'
trace libmamba Compute configurable 'use_default_prefix_fallback'
trace libmamba Compute configurable 'use_root_prefix_fallback'
trace libmamba Compute configurable 'use_target_prefix_fallback'
trace libmamba Compute configurable 'target_prefix'
trace libmamba Get RC files configuration from locations up to TargetPrefix
trace libmamba Configuration not found at '/usr/share/miniconda/envs/cgat-flow/.mambarc'
trace libmamba Configuration not found at '/usr/share/miniconda/envs/cgat-flow/condarc.d'
trace libmamba Configuration not found at '/usr/share/miniconda/envs/cgat-flow/condarc'
trace libmamba Configuration not found at '/usr/share/miniconda/envs/cgat-flow/.condarc'
trace libmamba Configuration not found at '/home/runner/.mambarc'
trace libmamba Configuration not found at '/home/runner/.mamba/mambarc.d'
trace libmamba Configuration not found at '/home/runner/.mamba/mambarc'
trace libmamba Configuration not found at '/home/runner/.mamba/.mambarc'
trace libmamba Configuration not found at '/home/runner/.config/mamba/mambarc.d'
trace libmamba Configuration not found at '/home/runner/.config/mamba/mambarc'
trace libmamba Configuration not found at '/home/runner/.config/mamba/.mambarc'
trace libmamba Configuration found at '/home/runner/.condarc'
trace libmamba Configuration not found at '/home/runner/.conda/condarc.d'
trace libmamba Configuration not found at '/home/runner/.conda/condarc'
trace libmamba Configuration not found at '/home/runner/.conda/.condarc'
trace libmamba Configuration not found at '/home/runner/.config/conda/condarc.d'
trace libmamba Configuration not found at '/home/runner/.config/conda/condarc'
trace libmamba Configuration not found at '/home/runner/.config/conda/.condarc'
trace libmamba Configuration not found at '/usr/share/miniconda/.mambarc'
trace libmamba Configuration not found at '/usr/share/miniconda/condarc.d'
trace libmamba Configuration not found at '/usr/share/miniconda/condarc'
trace libmamba Configuration found at '/usr/share/miniconda/.condarc'
trace libmamba Configuration not found at '/var/lib/conda/.mambarc'
trace libmamba Configuration not found at '/var/lib/conda/condarc.d/'
trace libmamba Configuration not found at '/var/lib/conda/condarc'
trace libmamba Configuration not found at '/var/lib/conda/.condarc'
trace libmamba Configuration not found at '/etc/conda/.mambarc'
trace libmamba Configuration not found at '/etc/conda/condarc.d/'
trace libmamba Configuration not found at '/etc/conda/condarc'
trace libmamba Configuration not found at '/etc/conda/.condarc'
trace libmamba Update configurable 'no_env'
trace libmamba Compute configurable 'relocate_prefix'
trace libmamba Compute configurable 'target_prefix_checks'
error libmamba No prefix found at: /usr/share/miniconda/envs/cgat-flow
error libmamba Environment must first be created with "mamba create -n {env_name} ..."
critical libmamba Aborting.
info libmamba ****************** Backtrace End ********************
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