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add further R scripts, moved #139

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add further R scripts, moved

add further R scripts, moved #139

Triggered via push December 11, 2024 18:16
@jscaberjscaber
pushed 00dffe9
JS-exome
Status Failure
Total duration 51s
Artifacts –

cgatflow_python.yml

on: push
Matrix: build
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1 error and 5 warnings
Ex1 (3.7, ubuntu-latest)
The process '/usr/share/miniconda/condabin/mamba' failed with exit code 1
Ex1 (3.7, ubuntu-latest)
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/
Ex1 (3.7, ubuntu-latest)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Ex1 (3.7, ubuntu-latest)
Mamba support is still experimental and can result in differently solved environments!
Ex1 (3.7, ubuntu-latest)
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'
Ex1 (3.7, ubuntu-latest)
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 ********************