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New CI flow: Check package against specific CRAN snapshot(s). (#25)
* Adds a new subflow which checks the package against specific cran snapshot(s) * Adds CI-CD badges.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,220 @@ | ||
| name: 'setup-r-dependencies' | ||
| description: 'Action to setup installation tools and install R dependencies' | ||
| author: 'Jim Hester (modified by Henrik Spiegelhauer)' | ||
| inputs: | ||
| cache: | ||
| description: 'A boolean value indicating whether packages should be cached from one to the other' | ||
| required: true | ||
| default: true | ||
| cache-version: | ||
| description: 'The version of the cache, change this from the default (1) to start over with a fresh cache. Ignored if cache: false' | ||
| required: true | ||
| default: 1 | ||
| extra-packages: | ||
| description: 'Any extra packages to install outside of the packages listed in the dependencies' | ||
| needs: | ||
| description: 'Any extra Config/Needs fields which need to be included when installing dependencies' | ||
| packages: | ||
| description: 'Which package(s) to install.' | ||
| default: 'deps::., any::sessioninfo' | ||
| pak-version: | ||
| description: 'Which pak version to use. Possible values are "stable", "rc" and "devel".' | ||
| default: 'stable' | ||
| working-directory: | ||
| description: 'Using the working-directory keyword, you can specify the working directory of where "pkg_deps" command searches for dependencies in the "DESCRIPTION" file.' | ||
| default: '.' | ||
| dependencies: | ||
| description: 'Types of dependencies to install. Must be an R expression. Note that it often needs to be quoted in YAML, see the README for details.' | ||
| default: '"all"' | ||
| dependency_repo: | ||
| description: 'Overwrite the default CRAN-like reposity' | ||
| default: 'NULL' | ||
| upgrade: | ||
| description: 'Whether to install the latest available versions of the dependencies. Must be an R expression. See the README for details if you need quoting.' | ||
| default: 'FALSE' | ||
| lockfile-create-lib: | ||
| description: 'The package library to consider when creating the pak lockfile. This is passed to the `lib` argument of `pak::lockfile_create()`. Defaults to an empty library, for reproducibility. Must be an R expression. Note that it often needs to be quoted in YAML, see the README for details.' | ||
| default: 'NULL' | ||
| install-pandoc: | ||
| description: 'Whether to install pandoc. By default it is installed if it is not on the PATH and the local package suggests or depends on the rmarkdown package.' | ||
| pandoc-version: | ||
| description: 'Pandoc version to install.' | ||
| default: '3.1.11' | ||
| runs: | ||
| using: "composite" | ||
| steps: | ||
| - name: Set site library path | ||
| run: | | ||
| # Set site library path | ||
| cat("::group::Set site library path\n") | ||
| if (Sys.getenv("RENV_PROJECT") != "") { | ||
| message("renv project detected, no need to set R_LIBS_SITE") | ||
| cat(sprintf("R_LIB_FOR_PAK=%s\n", .libPaths()[1]), file = Sys.getenv("GITHUB_ENV"), append = TRUE) | ||
| q("no") | ||
| } | ||
| lib <- Sys.getenv("R_LIBS_SITE") | ||
| if (lib == "") { | ||
| lib <- file.path(dirname(.Library), "site-library") | ||
| cat(sprintf("R_LIBS_SITE=%s\n", lib), file = Sys.getenv("GITHUB_ENV"), append = TRUE) | ||
| cat(sprintf("R_LIB_FOR_PAK=%s\n", lib), file = Sys.getenv("GITHUB_ENV"), append = TRUE) | ||
| message("Setting R_LIBS_SITE to ", lib) | ||
| } else { | ||
| message("R_LIBS_SITE is already set to ", lib) | ||
| cat(sprintf("R_LIB_FOR_PAK=%s\n", strsplit(lib, .Platform$path.sep)[[1]][[1]]), file = Sys.getenv("GITHUB_ENV"), append = TRUE) | ||
| } | ||
| cat("::endgroup::\n") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install pak (Windows) | ||
| if: runner.os == 'Windows' | ||
| run: | | ||
| # Install pak | ||
| cat("::group::Install pak\n") | ||
| lib <- Sys.getenv("R_LIB_FOR_PAK") | ||
| dir.create(lib, showWarnings = FALSE, recursive = TRUE) | ||
| install.packages("pak", lib = lib, repos = sprintf( | ||
| "https://r-lib.github.io/p/pak/%s/%s/%s/%s", | ||
| "${{ inputs.pak-version }}", | ||
| .Platform$pkgType, | ||
| R.Version()$os, | ||
| R.Version()$arch | ||
| )) | ||
| cat("::endgroup::\n") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install pak (Unix) | ||
| if: runner.os != 'Windows' | ||
| run: | | ||
| # Install pak | ||
| echo "::group::Install pak" | ||
| if which sudo >/dev/null; then SUDO="sudo -E --preserve-env=PATH env"; else SUDO=""; fi | ||
| $SUDO R -q -e 'dir.create(Sys.getenv("R_LIB_FOR_PAK"), recursive = TRUE, showWarnings = FALSE)' | ||
| $SUDO R -q -e 'install.packages("pak", lib = Sys.getenv("R_LIB_FOR_PAK"), repos = sprintf("https://r-lib.github.io/p/pak/%s/%s/%s/%s", "${{ inputs.pak-version }}", .Platform$pkgType, R.Version()$os, R.Version()$arch))' | ||
| echo "::endgroup::" | ||
| shell: bash | ||
|
|
||
| - name: Query dependencies | ||
| id: install | ||
| run: | | ||
| # Override the default CRAN-like repository | ||
| if ("${{ inputs.dependency_repo }}" != "NULL") { | ||
| options(repos = c(CRAN = "${{ inputs.dependency_repo }}")) | ||
| } | ||
| # Dependency resolution | ||
| cat("::group::Dependency resolution\n") | ||
| cat("os-version=", sessionInfo()$running, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) | ||
| r_version <- | ||
| if (grepl("development", R.version.string)) { | ||
| pdf(tempfile()) | ||
| ge_ver <- attr(recordPlot(), "engineVersion") | ||
| dev.off() | ||
| paste0("R version ", getRversion(), " (ge:", ge_ver, "; iid:", .Internal(internalsID()), ")") | ||
| } else { | ||
| R.version.string | ||
| } | ||
| cat("r-version=", r_version, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) | ||
| needs <- sprintf("Config/Needs/%s", strsplit("${{ inputs.needs }}", "[[:space:],]+")[[1]]) | ||
| deps <- strsplit("${{ inputs.packages }}", "[[:space:],]+")[[1]] | ||
| extra_deps <- strsplit("${{ inputs.extra-packages }}", "[[:space:],]+")[[1]] | ||
| dir.create(".github", showWarnings=FALSE) | ||
| Sys.setenv("PKGCACHE_HTTP_VERSION" = "2") | ||
| library(pak, lib.loc = Sys.getenv("R_LIB_FOR_PAK")) | ||
| pak::lockfile_create( | ||
| c(deps, extra_deps), | ||
| lockfile = ".github/pkg.lock", | ||
| upgrade = (${{ inputs.upgrade }}), | ||
| dependencies = c(needs, (${{ inputs.dependencies }})), | ||
| lib = ${{ inputs.lockfile-create-lib }} | ||
| ) | ||
| cat("::endgroup::\n") | ||
| cat("::group::Show Lockfile\n") | ||
| writeLines(readLines(".github/pkg.lock")) | ||
| cat("::endgroup::\n") | ||
| shell: Rscript {0} | ||
| working-directory: ${{ inputs.working-directory }} | ||
|
|
||
| - name: Restore R package cache | ||
| if: inputs.cache == 'true' | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ${{ env.R_LIBS_USER }}/* | ||
| !${{ env.R_LIBS_USER }}/pak | ||
| key: ${{ format('{0}-{1}-{2}-{3}', steps.install.outputs.os-version, steps.install.outputs.r-version, inputs.cache-version, inputs.dependency_repo, hashFiles(format('{0}/.github/pkg.lock', inputs.working-directory ))) }} | ||
| restore-keys: ${{ steps.install.outputs.os-version }}-${{ steps.install.outputs.r-version }}-${{inputs.cache-version }}-${{inputs.dependency_repo }} | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| # Override the default CRAN-like repository | ||
| if ("${{ inputs.dependency_repo }}" != "NULL") { | ||
| options(repos = c(CRAN = "${{ inputs.dependency_repo }}")) | ||
| } | ||
| # Install/Update packages | ||
| cat("::group::Install/update packages\n") | ||
| Sys.setenv("PKGCACHE_HTTP_VERSION" = "2") | ||
| library(pak, lib.loc = Sys.getenv("R_LIB_FOR_PAK")) | ||
| pak::lockfile_install(".github/pkg.lock") | ||
| ## Clean up lock file | ||
| unlink(".github/pkg.lock") | ||
| cat("::endgroup::\n") | ||
| shell: Rscript {0} | ||
| working-directory: ${{ inputs.working-directory }} | ||
|
|
||
| - name: Check whether pandoc needs to be installed | ||
| id: check-pandoc | ||
| run: | | ||
| cat("::group::Check if package needs pandoc\n") | ||
| o <- '${{ inputs.install-pandoc }}' | ||
| if (! o %in% c('true', 'false')) { | ||
| if (Sys.which("pandoc") != "") { | ||
| o <- 'false' | ||
| } else if (file.exists("DESCRIPTION")) { | ||
| deptypes <- list(direct = "all", indirect = character()) | ||
| deps <- pak::pkg_deps(".", dependencies = deptypes) | ||
| if ("rmarkdown" %in% deps$package) { | ||
| o <- 'true' | ||
| } else { | ||
| o <- 'false' | ||
| } | ||
| } else { | ||
| o <- 'false' | ||
| } | ||
| } | ||
| cat("install=", o, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) | ||
| cat("::endgroup::\n") | ||
| shell: Rscript {0} | ||
| working-directory: ${{ inputs.working-directory }} | ||
|
|
||
| - name: Install pandoc if needed | ||
| if: ${{ steps.check-pandoc.outputs.install == 'true' }} | ||
| uses: r-lib/actions/setup-pandoc@v2 | ||
| with: | ||
| pandoc-version: ${{ inputs.pandoc-version }} | ||
|
|
||
| - name: Session info | ||
| run: | | ||
| # Session info | ||
| cat("::group::Session info\n") | ||
| if (requireNamespace("sessioninfo", quietly = TRUE)) { | ||
| if (packageVersion("sessioninfo") >= "1.2.1") { | ||
| sessioninfo::session_info(pkgs = "installed", include_base = TRUE) | ||
| } else { | ||
| options(width = 200) | ||
| sessioninfo::session_info(rownames(installed.packages()), include_base=TRUE) | ||
| } | ||
| } else { | ||
| sessionInfo() | ||
| } | ||
| cat("::endgroup::\n") | ||
| shell: Rscript {0} | ||
| working-directory: ${{ inputs.working-directory }} | ||
|
|
||
| - name: Don't use tar 1.30 from Rtools35 to store the cache | ||
| if: runner.os == 'Windows' | ||
| shell: bash | ||
| run: | | ||
| if command -v /c/Rtools/bin/tar && /c/Rtools/bin/tar --version | grep -q 'tar (GNU tar) 1.30' | ||
| then echo 'C:/Program Files/Git/usr/bin' >> $GITHUB_PATH | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| --- | ||
| # R-CMD check which allows you to lock the R version and date of the CRAN snapshot. | ||
| # This is particularly helpful for ensuring that the package works with internal systems. | ||
| on: | ||
| workflow_dispatch: | ||
| workflow_call: | ||
|
|
||
| name: R-CMD-check-versions | ||
|
|
||
| jobs: | ||
| R-CMD-check: | ||
| runs-on: ${{ matrix.os }} | ||
| name: ${{ matrix.os }} (R ${{ matrix.config.r }}, CRAN ${{ matrix.config.date }}) | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| os: | ||
| - macos-latest | ||
| - windows-latest | ||
| - ubuntu-latest | ||
| config: | ||
| - date: 'latest' | ||
| r: 'release' | ||
| - date: 2023-10-25 # Lock the date of the CRAN snapshot | ||
| r: 4.3.1 | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| R_KEEP_PKG_SOURCE: yes | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: r-lib/actions/setup-pandoc@v2 | ||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
| use-public-rspm: false | ||
|
|
||
| - name: Determine the CRAN image to use | ||
| id: cran-image | ||
| run: | | ||
| if [ "${{ matrix.config.date }}" == "latest" ]; then | ||
| echo "image=https://cloud.r-project.org" >> $GITHUB_OUTPUT | ||
| else | ||
| echo "image=https://packagemanager.posit.co/cran/${{ matrix.config.date }}" >> $GITHUB_OUTPUT | ||
| fi | ||
| shell: bash | ||
|
|
||
| - name: Debug image | ||
| run: | | ||
| echo ${{ steps.cran-image.outputs.image }} | ||
| shell: bash | ||
|
|
||
| - name: Install R dependencies (custom) | ||
| uses: ./.github/actions/setup-r-dependencies | ||
| with: | ||
| cache: true | ||
| dependency_repo: ${{ steps.cran-image.outputs.image }} | ||
| working-directory: ${{ github.workspace }} | ||
| extra-packages: any::rcmdcheck | ||
|
|
||
| - name: Session info | ||
| run: | | ||
| sessionInfo() | ||
| installed.packages()[,c("Package", "Version")] | ||
| shell: Rscript {0} | ||
|
|
||
| - uses: r-lib/actions/check-r-package@v2 | ||
| with: | ||
| args: 'c("--no-manual", "--as-cran")' | ||
| upload-snapshots: true | ||
| error-on: '"error"' | ||
| check-dir: '"check"' | ||
| upload-results: true |
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