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Set R_BIOC_VERSION env variable used by pak #7

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merged 2 commits into from
Oct 20, 2022
Merged

Set R_BIOC_VERSION env variable used by pak #7

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7f79205
Set `R_BIOC_VERSION` env variable used by pak
milanmlft Oct 10, 2022
9f12ec8
Merge branch 'main' into fix-bioc-version
grimbough Oct 20, 2022
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10 changes: 6 additions & 4 deletions setup-bioc/action.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,25 +27,27 @@ runs:
echo "r-version=$(echo ${RVERSION})" >> $GITHUB_OUTPUT
echo "rtools-version=$(echo ${RTOOLS})" >> $GITHUB_OUTPUT
echo "bioc-version=$(echo ${BIOCVERSION})" >> $GITHUB_OUTPUT
echo "R_BIOC_VERSION=${BIOCVERSION}" >> $GITHUB_ENV

shell: bash

- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ steps.find-versions.outputs.r-version }}
Ncpus: ${{ inputs.Ncpus }}
use-public-rspm: ${{ inputs.use-public-rspm }}
rtools-version: ${{ steps.find-versions.outputs.rtools-version }}

- name: Download Renviron
run: |
download.file('https://bioconductor.org/checkResults/${{ inputs.bioc-version }}/bioc-LATEST/Renviron.bioc', destfile = '~/.Renviron', mode = 'wb')
shell: Rscript {0}

- name: Setting Bioconductor mirror
run: |
write('options(BioC_mirror = "${{ inputs.bioc-mirror }}")', file = '~/.Rprofile', append = TRUE)
shell: Rscript {0}

- name: Install and initialize BiocManager
run: |
install.packages(c("BiocManager", "remotes"), quiet = TRUE)
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