-
Notifications
You must be signed in to change notification settings - Fork 31
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Oscar Kjell
authored and
Oscar Kjell
committed
Nov 26, 2024
1 parent
62ff31e
commit 169946a
Showing
4 changed files
with
358 additions
and
68 deletions.
There are no files selected for viewing
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
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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,84 +1,144 @@ | ||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| branches: [ "master" ] | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| branches: [ "master" ] | ||
|
|
||
| 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: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com"} | ||
| - {os: windows-latest, r: 'release'} | ||
| - {os: macOS-latest, r: 'release'} | ||
| - {os: windows-latest, r: 'release'} | ||
| - {os: ubuntu-20.04, r: 'release'} | ||
|
|
||
| env: | ||
| ACTIONS_ALLOW_UNSECURE_COMMANDS: true | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| RSPM: ${{ matrix.config.rspm }} | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| R_LIBS_USER: /tmp/Library | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v2 | ||
|
|
||
| - name: Set up R | ||
| uses: r-lib/actions/setup-r@v2-branch | ||
| # macOS-specific steps | ||
| - name: Fix and Debug Homebrew Issues | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| # Reset Homebrew changes | ||
| cd /opt/homebrew/Library/Taps/homebrew/homebrew-core || exit 1 | ||
| git stash -u || echo "No changes to stash" | ||
| git clean -d -f || echo "No files to clean" | ||
| # Fix Homebrew permissions | ||
| sudo chown -R $(whoami) $(brew --prefix)/* | ||
| # Debug Homebrew | ||
| brew doctor || echo "brew doctor failed" | ||
| brew config || echo "brew config failed" | ||
| - name: Install macOS Utilities | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| brew update || echo "Homebrew update failed" | ||
| brew install libomp || echo "libomp installation failed" | ||
| brew install qpdf || echo "qpdf installation failed but continuing" | ||
| export DYLD_LIBRARY_PATH=$(brew --prefix libomp)/lib | ||
| echo "DYLD_LIBRARY_PATH=$(brew --prefix libomp)/lib" >> $GITHUB_ENV | ||
| # Set up R environment | ||
| - uses: r-lib/actions/setup-r@v2-branch | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
|
|
||
| - name: Install system dependencies (Ubuntu) | ||
| - uses: r-lib/actions/setup-pandoc@v2-branch | ||
|
|
||
| # Install Miniconda (all OS) | ||
| - uses: conda-incubator/setup-miniconda@v3 | ||
| with: | ||
| auto-update-conda: true | ||
| python-version: 3.9 | ||
| miniconda-version: "latest" | ||
|
|
||
| - name: Install Conda Dependencies | ||
| run: | | ||
| conda config --add channels defaults | ||
| conda config --set solver classic | ||
| conda install -c conda-forge numpy | ||
| - name: Query R Dependencies | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
|
|
||
| # Cache R packages | ||
| - name: Cache R Packages | ||
| if: runner.os != 'Windows' | ||
| uses: actions/cache@v1 | ||
| with: | ||
| path: ${{ env.R_LIBS_USER }} | ||
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | ||
|
|
||
| # Install system dependencies (Linux only) | ||
| - name: Install System Dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| sudo apt-get update -y | ||
| sudo apt-get install -y libcurl4-openssl-dev libxml2-dev libssl-dev | ||
| sudo apt-get install -y libharfbuzz-dev libfribidi-dev | ||
| sudo apt-get install -y pandoc | ||
| shell: bash | ||
| while read -r cmd; do | ||
| eval sudo $cmd | ||
| done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")') | ||
| sudo apt install libharfbuzz-dev libfribidi-dev | ||
| - name: Set up Pandoc | ||
| uses: r-lib/actions/setup-pandoc@v2-branch | ||
| # Install R dependencies | ||
| - name: Install R Dependencies | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE) | ||
| remotes::install_cran("rcmdcheck") | ||
| shell: Rscript {0} | ||
|
|
||
| # Fix Conda permissions (macOS only) | ||
| - name: Fix Conda Permissions | ||
| if: runner.os == 'macOS' | ||
| run: sudo chown -R $UID $CONDA | ||
|
|
||
| - name: Install required R packages | ||
| # Install and test "text" package | ||
| - name: Install and Test "text" Package | ||
| run: | | ||
| options(repos = c(CRAN = "https://cran.rstudio.com")) | ||
| install.packages("remotes") | ||
| remotes::install_cran(c( | ||
| "topics", "rcmdcheck", "devtools", "dplyr", "tidyr", "ggplot2", | ||
| "ggrepel", "cowplot", "parsnip", "recipes", "rsample", | ||
| "reticulate", "tune", "workflows", "yardstick", | ||
| "future", "furrr", "rmarkdown", "evaluate" | ||
| )) | ||
| install.packages("devtools") | ||
| library(devtools) | ||
| devtools::install_github("oscarkjell/text") | ||
| text::textrpp_install(prompt = FALSE) | ||
| text::textrpp_initialize(textEmbed_test = TRUE) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Verify installed packages | ||
| # Session Info | ||
| - name: Session Info | ||
| run: | | ||
| required_packages <- c( | ||
| "topics", "rcmdcheck", "devtools", "dplyr", "tidyr", "ggplot2", | ||
| "ggrepel", "cowplot", "parsnip", "recipes", "rsample", | ||
| "reticulate", "tune", "workflows", "yardstick", | ||
| "future", "furrr", "rmarkdown", "evaluate" | ||
| ) | ||
| not_installed <- setdiff(required_packages, rownames(installed.packages())) | ||
| if (length(not_installed) > 0) { | ||
| stop("Some required packages are not installed: ", paste(not_installed, collapse = ", ")) | ||
| } | ||
| options(width = 100) | ||
| pkgs <- installed.packages()[, "Package"] | ||
| sessioninfo::session_info(pkgs, include_base = TRUE) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Run R CMD Check | ||
| # Run R CMD check | ||
| - name: R CMD Check | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_: false | ||
| run: | | ||
| rcmdcheck::rcmdcheck( | ||
| args = c("--no-manual", "--as-cran"), | ||
| build_args = "--no-build-vignettes" | ||
| ) | ||
| OMP_MAX_ACTIVE_LEVELS: 0 | ||
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | ||
| shell: Rscript {0} | ||
|
|
||
| # Display testthat output | ||
| - name: Display Testthat Output | ||
| if: always() | ||
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | ||
| shell: bash |
Oops, something went wrong.