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Try to fix spacing on the yaml file
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.github/workflows/check-bioc.yml

Lines changed: 21 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -44,27 +44,27 @@ env:
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jobs:
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bioc-config:
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runs-on: ubuntu-latest
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outputs:
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matrix: ${{ steps.set-matrix.outputs.matrix }}
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steps:
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- id: set-bioc-matrix
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run: |
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bioc=$(curl -L https://bioconductor.org/config.yaml)
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if [[ "$latest_release" == "true" ]]; then
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echo "Finding the latest BioC release version and the corresponding R version"
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biocversion=$(echo $bioc | grep "release_version: " | grep -Eo "[0-9]{1}\.[0-9]{2}")
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rversion=$(echo $bioc | grep "r_version_associated_with_release: " | grep -Eo "[0-9]{1}\.[0-9]{1}")
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biocmajor=$(echo $biocversion | cut -c 1-1)
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biocminor=$(echo $biocversion | cut -c 3-4)
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bioccont="bioconductor/bioconductor_docker:RELEASE_${biocmajor}_${biocminor}"
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else
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echo "Finding the latest BioC devel version and the corresponding R version"
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biocversion=$(echo $bioc | grep "devel_version: " | grep -Eo "[0-9]{1}\.[0-9]{2}")
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rversion=$(echo $bioc | grep "r_version_associated_with_devel: " | grep -Eo "[0-9]{1}\.[0-9]{1}")
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bioccont="bioconductor/bioconductor_docker:devel"
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fi
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echo "matrix={ \"config\": { [{\"os\" : \"ubuntu-latest\", \"r\" : \"${rversion}\", \"bioc\" : \"${biocversion}\", \"cont\" : \"${bioccont}\"} , {\"os\" : \"macOS-latest\", \"r\" : \"${rversion}\", \"bioc\" : \"${biocversion}\"} , {\"os\" : \"windows-latest\", \"r\" : \"${rversion}\", \"bioc\" : \"${biocversion}\" }] } }"
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runs-on: ubuntu-latest
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outputs:
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matrix: ${{ steps.set-matrix.outputs.matrix }}
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steps:
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- id: set-bioc-matrix
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run: |
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bioc=$(curl -L https://bioconductor.org/config.yaml)
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if [[ "$latest_release" == "true" ]]; then
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echo "Finding the latest BioC release version and the corresponding R version"
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biocversion=$(echo $bioc | grep "release_version: " | grep -Eo "[0-9]{1}\.[0-9]{2}")
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rversion=$(echo $bioc | grep "r_version_associated_with_release: " | grep -Eo "[0-9]{1}\.[0-9]{1}")
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biocmajor=$(echo $biocversion | cut -c 1-1)
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biocminor=$(echo $biocversion | cut -c 3-4)
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bioccont="bioconductor/bioconductor_docker:RELEASE_${biocmajor}_${biocminor}"
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else
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echo "Finding the latest BioC devel version and the corresponding R version"
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biocversion=$(echo $bioc | grep "devel_version: " | grep -Eo "[0-9]{1}\.[0-9]{2}")
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rversion=$(echo $bioc | grep "r_version_associated_with_devel: " | grep -Eo "[0-9]{1}\.[0-9]{1}")
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bioccont="bioconductor/bioconductor_docker:devel"
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fi
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echo "matrix={ \"config\": { [{\"os\" : \"ubuntu-latest\", \"r\" : \"${rversion}\", \"bioc\" : \"${biocversion}\", \"cont\" : \"${bioccont}\"} , {\"os\" : \"macOS-latest\", \"r\" : \"${rversion}\", \"bioc\" : \"${biocversion}\"} , {\"os\" : \"windows-latest\", \"r\" : \"${rversion}\", \"bioc\" : \"${biocversion}\" }] } }"
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build-check:
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needs: bioc-config

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