Fix logging level for SNP filter script #46
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11 warnings
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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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/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:200: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:
conda config --add channels defaults
For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
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The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
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++ dirname -- /home/runner/miniconda3/envs/stemcnv-check-general-R/bin/installBiocDataPackage.sh
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+ SCRIPT_DIR=/home/runner/miniconda3/envs/stemcnv-check-general-R/bin/../share/bioconductor-data-packages
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+ json=/home/runner/miniconda3/envs/stemcnv-check-general-R/bin/../share/bioconductor-data-packages/dataURLs.json
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++ yq '."genomeinfodbdata-1.2.11".fn' /home/runner/miniconda3/envs/stemcnv-check-general-R/bin/../share/bioconductor-data-packages/dataURLs.json
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+ FN='"GenomeInfoDbData_1.2.11.tar.gz"'
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+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.11".urls[]' /home/runner/miniconda3/envs/stemcnv-check-general-R/bin/../share/bioconductor-data-packages/dataURLs.json
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+ URLS+=($value)
+ IFS=
+ read -r value
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+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
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