binary and time-to-event informed priors (#29) #161
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on: | |
| push: | |
| branches: | |
| - main | |
| - master | |
| - pre-release | |
| pull_request: | |
| branches: | |
| - main | |
| - master | |
| - pre-release | |
| 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: windows-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| # - {os: macOS-latest, r: 'release'} | |
| # - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| # - {os: ubuntu-latest, r: 'oldrel-1'} | |
| env: | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: false | |
| NOT_CRAN: true | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3- | |
| - name: Set path for RTools 4.0 | |
| if: runner.os == 'Windows' | |
| run: echo "C:/rtools40/usr/bin;C:/rtools40/mingw64/bin" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8 | |
| - name: Install most Windows system dependencies | |
| if: runner.os == 'Windows' | |
| run: | | |
| pacman -Syu mingw-w64-x86_64-make --noconfirm | |
| g++ --version | |
| Get-Command g++ | Select-Object -ExpandProperty Definition | |
| mingw32-make --version | |
| Get-Command mingw32-make | Select-Object -ExpandProperty Definition | |
| (New-Object System.Net.WebClient).DownloadFile('https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/JAGS-4.3.1.exe', 'C:\JAGS-4.3.1.exe') | |
| shell: powershell | |
| - name: Install JAGS on Windows | |
| if: runner.os == 'Windows' | |
| run: C:\JAGS-4.3.1.exe /S | |
| shell: cmd | |
| - name: Install Linux system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| sudo apt-get install -y libglpk-dev | |
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | |
| sudo -s eval "$sysreqs" | |
| sudo -s apt-get install jags | |
| sudo -s apt-get install libv8-dev | |
| sudo -s apt-get install libnode-dev | |
| sudo -s apt-get install libcurl4-openssl-dev | |
| - name: Install Mac system dependencies | |
| if: runner.os == 'macOS' | |
| run: | | |
| rm '/usr/local/bin/gfortran' | |
| brew install automake jags | |
| - name: Install dependencies | |
| if: runner.os != 'macOS' | |
| run: | | |
| remotes::install_deps(dependencies = TRUE, type = ifelse(tolower(Sys.info()["sysname"]) == "linux", "source", "binary")) | |
| remotes::install_cran("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Install dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| remotes::install_deps(dependencies = TRUE, type = ifelse(tolower(Sys.info()["sysname"]) == "linux", "source", "binary")) | |
| install.packages("rjags", type = "source") | |
| remotes::install_cran("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Check | |
| if: runner.os != 'Windows' | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: | | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-manual", "--as-cran", "--ignore-vignettes"), | |
| build_args = c("--no-build-vignettes"), | |
| error_on = "warning", | |
| check_dir = "check") | |
| shell: Rscript {0}" | |
| - name: Check | |
| if: runner.os == 'Windows' | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| JAGS_ROOT: "/c/progra~1/JAGS/JAGS-4.3.1" | |
| JAGS_MAJOR_VERSION: 4 | |
| run: | | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-manual", "--as-cran", "--ignore-vignettes"), | |
| build_args = c("--no-build-vignettes"), | |
| error_on = "warning", | |
| check_dir = "check") | |
| shell: Rscript {0}" | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check |