handle inf loglik, no default penalty for restarts, bootstrap seqeuen… #107
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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: | |
| push: | |
| branches: [main, nhmm] | |
| pull_request: | |
| branches: [main, nhmm] | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macos-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'oldrel-1'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| # this sets the env variable to true or false depending on whether the | |
| # commit message contains text 'run-extended' | |
| SEQHMM_EXTENDED_TESTS: ${{contains(github.event.head_commit.message, 'run-extended')}} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-tinytex@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: | |
| any::rcmdcheck | |
| any::tinytex | |
| - name: Install dependencies | |
| run: | | |
| tinytex::parse_install(text = "! LaTeX Error: File `ae.sty' not found.") | |
| tinytex::parse_install(text = "! LaTeX Error: File `grfext.sty' not found.") | |
| tinytex::tlmgr_install("babel-english") | |
| shell: Rscript {0} | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| args: 'c("--as-cran", "--no-manual", "--no-vignettes", "--no-build-vignettes", "--ignore-vignettes")' | |
| build_args: 'c("--no-build-vignettes")' | |