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| 1 | +## Read more about GitHub actions the features of this GitHub Actions workflow |
| 2 | +## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action |
| 3 | +## |
| 4 | +## For more details, check the biocthis developer notes vignette at |
| 5 | +## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html |
| 6 | +## |
| 7 | +## You can add this workflow to other packages using: |
| 8 | +## > biocthis::use_bioc_github_action() |
| 9 | +## |
| 10 | +## Using GitHub Actions exposes you to many details about how R packages are |
| 11 | +## compiled and installed in several operating system.s |
| 12 | +### If you need help, please follow the steps listed at |
| 13 | +## https://github.com/r-lib/actions#where-to-find-help |
| 14 | +## |
| 15 | +## If you found an issue specific to biocthis's GHA workflow, please report it |
| 16 | +## with the information that will make it easier for others to help you. |
| 17 | +## Thank you! |
| 18 | + |
| 19 | +## Acronyms: |
| 20 | +## * GHA: GitHub Action |
| 21 | +## * OS: operating system |
| 22 | + |
| 23 | +on: |
| 24 | + push: |
| 25 | + pull_request: |
| 26 | + |
| 27 | +name: R-CMD-check-bioc |
| 28 | + |
| 29 | +## These environment variables control whether to run GHA code later on that is |
| 30 | +## specific to testthat, covr, and pkgdown. |
| 31 | +## |
| 32 | +## If you need to clear the cache of packages, update the number inside |
| 33 | +## cache-version as discussed at https://github.com/r-lib/actions/issues/86. |
| 34 | +## Note that you can always run a GHA test without the cache by using the word |
| 35 | +## "/nocache" in the commit message. |
| 36 | +env: |
| 37 | + has_testthat: 'true' |
| 38 | + run_covr: 'true' |
| 39 | + run_pkgdown: 'false' |
| 40 | + has_RUnit: 'false' |
| 41 | + cache-version: 'cache-v1' |
| 42 | + |
| 43 | +jobs: |
| 44 | + build-check: |
| 45 | + runs-on: ${{ matrix.config.os }} |
| 46 | + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) |
| 47 | + container: ${{ matrix.config.cont }} |
| 48 | + ## Environment variables unique to this job. |
| 49 | + |
| 50 | + strategy: |
| 51 | + fail-fast: false |
| 52 | + matrix: |
| 53 | + config: |
| 54 | + - { os: ubuntu-latest, r: '4.0', bioc: '3.12', cont: "bioconductor/bioconductor_docker:RELEASE_3_12", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } |
| 55 | + - { os: macOS-latest, r: '4.0', bioc: '3.12'} |
| 56 | + - { os: windows-latest, r: '4.0', bioc: '3.12'} |
| 57 | + env: |
| 58 | + R_REMOTES_NO_ERRORS_FROM_WARNINGS: true |
| 59 | + RSPM: ${{ matrix.config.rspm }} |
| 60 | + NOT_CRAN: true |
| 61 | + TZ: UTC |
| 62 | + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |
| 63 | + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} |
| 64 | + |
| 65 | + steps: |
| 66 | + |
| 67 | + ## Set the R library to the directory matching the |
| 68 | + ## R packages cache step further below when running on Docker (Linux). |
| 69 | + - name: Set R Library home on Linux |
| 70 | + if: runner.os == 'Linux' |
| 71 | + run: | |
| 72 | + mkdir /__w/_temp/Library |
| 73 | + echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile |
| 74 | +
|
| 75 | + ## Most of these steps are the same as the ones in |
| 76 | + ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml |
| 77 | + ## If they update their steps, we will also need to update ours. |
| 78 | + - name: Checkout Repository |
| 79 | + uses: actions/checkout@v2 |
| 80 | + |
| 81 | + ## R is already included in the Bioconductor docker images |
| 82 | + - name: Setup R from r-lib |
| 83 | + if: runner.os != 'Linux' |
| 84 | + uses: r-lib/actions/setup-r@master |
| 85 | + with: |
| 86 | + r-version: ${{ matrix.config.r }} |
| 87 | + |
| 88 | + ## pandoc is already included in the Bioconductor docker images |
| 89 | + - name: Setup pandoc from r-lib |
| 90 | + if: runner.os != 'Linux' |
| 91 | + uses: r-lib/actions/setup-pandoc@master |
| 92 | + |
| 93 | + - name: Query dependencies |
| 94 | + run: | |
| 95 | + install.packages('remotes') |
| 96 | + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) |
| 97 | + shell: Rscript {0} |
| 98 | + |
| 99 | + - name: Cache R packages |
| 100 | + if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" |
| 101 | + uses: actions/cache@v2 |
| 102 | + with: |
| 103 | + path: ${{ env.R_LIBS_USER }} |
| 104 | + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }} |
| 105 | + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0- |
| 106 | + |
| 107 | + - name: Cache R packages on Linux |
| 108 | + if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " |
| 109 | + uses: actions/cache@v2 |
| 110 | + with: |
| 111 | + path: /home/runner/work/_temp/Library |
| 112 | + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }} |
| 113 | + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0- |
| 114 | + |
| 115 | + - name: Install Linux system dependencies |
| 116 | + if: runner.os == 'Linux' |
| 117 | + run: | |
| 118 | + sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))') |
| 119 | + echo $sysreqs |
| 120 | + sudo -s eval "$sysreqs" |
| 121 | +
|
| 122 | + - name: Install macOS system dependencies |
| 123 | + if: matrix.config.os == 'macOS-latest' |
| 124 | + run: | |
| 125 | + ## Enable installing XML from source if needed |
| 126 | + brew install libxml2 |
| 127 | + echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV |
| 128 | +
|
| 129 | + ## Required to install magick as noted at |
| 130 | + ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 |
| 131 | + brew install imagemagick@6 |
| 132 | +
|
| 133 | + ## For textshaping, required by ragg, and required by pkgdown |
| 134 | + brew install harfbuzz fribidi |
| 135 | +
|
| 136 | + ## See if this helps get RCurl installed |
| 137 | + ## brew uninstall curl |
| 138 | +
|
| 139 | + - name: Install Windows system dependencies |
| 140 | + if: runner.os == 'Windows' |
| 141 | + run: | |
| 142 | + ## Edit below if you have any Windows system dependencies |
| 143 | + shell: Rscript {0} |
| 144 | + |
| 145 | + - name: Install BiocManager |
| 146 | + run: | |
| 147 | + message(paste('****', Sys.time(), 'installing BiocManager ****')) |
| 148 | + remotes::install_cran("BiocManager") |
| 149 | + shell: Rscript {0} |
| 150 | + |
| 151 | + - name: Set BiocVersion |
| 152 | + run: | |
| 153 | + BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) |
| 154 | + shell: Rscript {0} |
| 155 | + |
| 156 | + - name: Install dependencies |
| 157 | + run: | |
| 158 | + ## Try installing the package dependencies in steps. First the local |
| 159 | + ## dependencies, then any remaining dependencies to avoid the |
| 160 | + ## issues described at |
| 161 | + ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html |
| 162 | + ## https://github.com/r-lib/remotes/issues/296 |
| 163 | + ## Ideally, all dependencies should get installed in the first pass. |
| 164 | +
|
| 165 | + ## Temporary for now due to https://github.com/ropensci/RefManageR/issues/79 |
| 166 | + remotes::install_github("ropensci/bibtex") |
| 167 | + remotes::install_github("ropensci/RefManageR") |
| 168 | + remotes::install_github("cboettig/knitcitations") |
| 169 | +
|
| 170 | + ## Pass #1 at installing dependencies |
| 171 | + message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) |
| 172 | + remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE) |
| 173 | +
|
| 174 | + ## Pass #2 at installing dependencies |
| 175 | + message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) |
| 176 | + remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE) |
| 177 | +
|
| 178 | + ## For running the checks |
| 179 | + message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) |
| 180 | + remotes::install_cran("rcmdcheck") |
| 181 | + BiocManager::install("BiocCheck") |
| 182 | + shell: Rscript {0} |
| 183 | + |
| 184 | + - name: Install BiocGenerics |
| 185 | + if: env.has_RUnit == 'true' |
| 186 | + run: | |
| 187 | + ## Install BiocGenerics |
| 188 | + BiocManager::install("BiocGenerics") |
| 189 | + shell: Rscript {0} |
| 190 | + |
| 191 | + - name: Install covr |
| 192 | + if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' |
| 193 | + run: | |
| 194 | + remotes::install_cran("covr") |
| 195 | + shell: Rscript {0} |
| 196 | + |
| 197 | + - name: Install pkgdown |
| 198 | + if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' |
| 199 | + run: | |
| 200 | + remotes::install_cran("pkgdown") |
| 201 | + shell: Rscript {0} |
| 202 | + |
| 203 | + - name: Session info |
| 204 | + run: | |
| 205 | + options(width = 100) |
| 206 | + pkgs <- installed.packages()[, "Package"] |
| 207 | + sessioninfo::session_info(pkgs, include_base = TRUE) |
| 208 | + shell: Rscript {0} |
| 209 | + |
| 210 | + - name: Run CMD check |
| 211 | + env: |
| 212 | + _R_CHECK_CRAN_INCOMING_: false |
| 213 | + run: | |
| 214 | + rcmdcheck::rcmdcheck( |
| 215 | + args = c("--no-build-vignettes", "--no-manual", "--timings"), |
| 216 | + build_args = c("--no-manual", "--no-resave-data"), |
| 217 | + error_on = "warning", |
| 218 | + check_dir = "check" |
| 219 | + ) |
| 220 | + shell: Rscript {0} |
| 221 | + |
| 222 | + ## Might need an to add this to the if: && runner.os == 'Linux' |
| 223 | + - name: Reveal testthat details |
| 224 | + if: env.has_testthat == 'true' |
| 225 | + run: find . -name testthat.Rout -exec cat '{}' ';' |
| 226 | + |
| 227 | + - name: Run RUnit tests |
| 228 | + if: env.has_RUnit == 'true' |
| 229 | + run: | |
| 230 | + BiocGenerics:::testPackage() |
| 231 | + shell: Rscript {0} |
| 232 | + |
| 233 | + - name: Run BiocCheck |
| 234 | + run: | |
| 235 | + BiocCheck::BiocCheck( |
| 236 | + dir('check', 'tar.gz$', full.names = TRUE), |
| 237 | + `quit-with-status` = TRUE, |
| 238 | + `no-check-R-ver` = TRUE, |
| 239 | + `no-check-bioc-help` = TRUE |
| 240 | + ) |
| 241 | + shell: Rscript {0} |
| 242 | + |
| 243 | + - name: Test coverage |
| 244 | + if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' |
| 245 | + run: | |
| 246 | + covr::codecov() |
| 247 | + shell: Rscript {0} |
| 248 | + |
| 249 | + - name: Install package |
| 250 | + if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' |
| 251 | + run: R CMD INSTALL . |
| 252 | + |
| 253 | + - name: Deploy package |
| 254 | + if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' |
| 255 | + run: | |
| 256 | + git config --local user.email "[email protected]" |
| 257 | + git config --local user.name "GitHub Actions" |
| 258 | + Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)" |
| 259 | + shell: bash {0} |
| 260 | + ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE) |
| 261 | + ## at least one locally before this will work. This creates the gh-pages |
| 262 | + ## branch (erasing anything you haven't version controlled!) and |
| 263 | + ## makes the git history recognizable by pkgdown. |
| 264 | + |
| 265 | + - name: Upload check results |
| 266 | + if: failure() |
| 267 | + uses: actions/upload-artifact@master |
| 268 | + with: |
| 269 | + name: ${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-results |
| 270 | + path: check |
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