Fix capture output #139
Workflow file for this run
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| # Download the stock synthesis executable, then Run r cmd check | |
| # Name of the workflow, which will be what it is called under the "actions" tab | |
| name: r-cmd-check | |
| # on specifies the build triggers. Learn more at https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows | |
| on: | |
| # The schedule build trigger runs the workflow at a scheduled time. | |
| schedule: | |
| # This should run the default branch (typically main) weekly on sunday at 2:45am UTC | |
| - cron: '01 3 * * 2' | |
| # The workflow_dispatch build trigger adds a button so that you can start workflows manually. | |
| workflow_dispatch: | |
| # The push build trigger runs jobs when new commits are pushed up to github. | |
| push: | |
| # specifying branches means the workflow will only run on pushes to the branches listed, in this case, only main | |
| branches: | |
| - main | |
| - r4ss_1.50.0 | |
| # The pull_request build trigger runs jobs when a pull request is made or commits are pushed to the pull request. | |
| pull_request: | |
| # specifying branches means the workflow will only run when the pull request is to the merge into the branch listed, in this case, main. | |
| branches: | |
| - main | |
| # jobs specifies the jobs to run. you can have multiple jobs per github actions workflow, but in this case we have only one, which is | |
| # named run-R-CMD-check. | |
| jobs: | |
| run-R-CMD-check: | |
| # the operating system to run on | |
| runs-on: 'ubuntu-latest' | |
| strategy: | |
| fail-fast: false | |
| # environment settings, needed for running r (first 2 settings) and downloading from github (GITHUB_PAT) | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout github repository, in this case nwfscDiags | |
| uses: actions/checkout@v3 | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| - name: Setup pandoc, in case of vignettes in the R package | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Setup R packages | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - name: Get the latest SS3 executable and move to expected location | |
| run: | | |
| wget -O ss3 https://github.com/nmfs-ost/ss3-source-code/releases/latest/download/ss3_linux | |
| sudo chmod a+x ss3 | |
| cp ss3 inst/extdata/simple_small/ss3 | |
| rm ss3 | |
| - name: run r-cmd-check using R | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: 'linux-release-results' | |
| path: check |