omics service error: could not resolve host #606
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| issue_comment: | |
| types: [created] | |
| name: Commands | |
| jobs: | |
| document: | |
| if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }} | |
| name: document | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/pr-fetch@v2 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::roxygen2 | |
| needs: pr-document | |
| - name: Document | |
| run: | | |
| roxygen2::roxygenise(package.dir = 'paws.common') | |
| shell: Rscript {0} | |
| - name: commit | |
| run: | | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" | |
| git add man/\* NAMESPACE | |
| git commit -m 'Document' | |
| - uses: r-lib/actions/pr-push@v2 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| style: | |
| if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }} | |
| name: style | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/pr-fetch@v2 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: r-lib/actions/setup-r@v2 | |
| - name: Install dependencies | |
| run: install.packages("styler") | |
| shell: Rscript {0} | |
| - name: Style | |
| run: | | |
| styler::style_pkg(pkg = 'paws.common') | |
| styler::style_pkg(pkg = 'make.paws') | |
| shell: Rscript {0} | |
| - name: commit | |
| run: | | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" | |
| git add \*.R | |
| git commit -m 'Style' | |
| - uses: r-lib/actions/pr-push@v2 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| version: | |
| if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/version') }} | |
| name: version | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| VERSION: ${{ github.event.comment.body }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/pr-fetch@v2 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: r-lib/actions/setup-r@v2 | |
| - name: Version | |
| id: version | |
| run: | | |
| # extract make.paws::paws_update_version to reduce the need to install make.paws | |
| paws_update_version <- function(dir) { | |
| var <- Sys.getenv("VERSION") | |
| m <- regexpr("[0-9\\.]+", var) | |
| version <- gsub('[[:punct:] ]$',"", regmatches(var, m, invert = FALSE)) | |
| cat("pkg_version=", version, "\n", sep="", file = Sys.getenv("GITHUB_OUTPUT")) | |
| packages <- list.files(dir, full.names = T) | |
| descriptions <- file.path(packages, "DESCRIPTION") | |
| if (length(version) == 0) return() | |
| for (desc in descriptions) { | |
| lines <- readLines(desc) | |
| found <- grepl("Version: [0-9\\.]+", lines, perl = T) | |
| lines[found] <- gsub("[0-9\\.]+", version, lines[found]) | |
| found <- grepl("paws\\..*[0-9]+\\.[0-9]+\\.[0-9]+", lines, | |
| perl = T) | |
| found[found] <- !grepl("paws\\.common.*[0-9]+\\.[0-9]+\\.[0-9]+", | |
| lines[found], perl = T) | |
| lines[found] <- gsub("[0-9]+\\.[0-9]+\\.[0-9]+", version, | |
| lines[found]) | |
| writeLines(lines, desc) | |
| } | |
| } | |
| paws_update_version("cran") | |
| shell: Rscript {0} | |
| - name: commit | |
| if: ${{ steps.version.outputs.pkg_version != '' }} | |
| run: | | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" | |
| git add cran/* | |
| git commit -m 'Update Cran Version: ${{ steps.version.outputs.pkg_version }}' | |
| - uses: r-lib/actions/pr-push@v2 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} |