Improve normalize performance #1689
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| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | |
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: [ master, dev ] | |
| pull_request: | |
| schedule: | |
| - cron: "0 6 * * 3" | |
| name: R Build and Checks | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-${{ matrix.config.os }} | |
| name: ubuntu-${{ matrix.config.os }} (${{ matrix.config.r }} / ${{ matrix.config.bioc }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| #- { os: 24.04, r: 'devel', bioc: '3.21' } # Bioc 3.21 (devel) requires R 4.5 | |
| - { os: 24.04, r: '4.4', bioc: '3.20', pkgdown: "true" } | |
| - { os: 22.04, r: '4.3', bioc: '3.18' } | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - 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-pandoc@v2 | |
| - name: Install pdflatex | |
| run: sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra | |
| - name: Install packages | |
| if: runner.os != 'Windows' | |
| # libharfbuzz-dev libfribidi-dev are added to fix textshaping install error | |
| # libhdf5-dev added for cellmembrane/SeuratDisk | |
| # libglpk-dev added due to igraph / bluster /scran error | |
| # NOTE: added numpy<2 to side-step a numpy version issue. This should be removed eventually. See: https://github.com/numpy/numpy/issues/26710 | |
| run: | | |
| # NOTE: libsodium-dev installed for VISION | |
| sudo apt-get update && sudo apt-get install -yq libharfbuzz-dev libfribidi-dev python3 python3-pip libsodium-dev libcurl4-openssl-dev libglpk-dev libhdf5-dev libmagick++-dev | |
| sudo apt-get update | |
| sudo apt-get install -yq libharfbuzz-dev libfribidi-dev libsodium-dev libcurl4-openssl-dev python3 python3-pip | |
| python3 -m pip install --user wheel setuptools | |
| python3 -m pip install --user "numpy<2.0.0" | |
| python3 -m pip install --user umap-learn phate sctour tcrdist3 scikit-misc leidenalg | |
| - name: Setup CoNGA | |
| run: | | |
| python3 -m pip install --user scanpy | |
| cd ../ | |
| git clone https://github.com/phbradley/conga.git conga | |
| cd conga/tcrdist_cpp | |
| make | |
| cd ../../ | |
| pip3 install -e conga | |
| cd CellMembrane | |
| - name: Setup SDA | |
| run: | | |
| SDA_PATH=/home/runner/work/sda | |
| mkdir $SDA_PATH | |
| wget -q -O $SDA_PATH/sda_static_linux https://www.dropbox.com/sh/chek4jkr28qnbrj/AADPy1qQlm3jsHPmPdNsjSx2a/bin/sda_static_linux?dl=1 | |
| chmod +x $SDA_PATH/sda_static_linux | |
| echo /home/runner/work/sda >> $GITHUB_PATH | |
| # Note: the environment variable R_BIOC_VERSION is set to force remotes::install_bioc to follow the proper version | |
| - name: Setup Bioconductor | |
| run: | | |
| install.packages('devtools') | |
| if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager"); | |
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE); | |
| cat(append = TRUE, file = "~/.Rprofile", "options(repos = BiocManager::repositories());") | |
| cat(append = TRUE, file = "~/.Rprofile", "Sys.setenv(R_BIOC_VERSION=as.character(BiocManager::version()));"); | |
| shell: Rscript {0} | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| print(paste0("R_BIOC_VERSION: ", Sys.getenv("R_BIOC_VERSION"))); | |
| 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} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-${{ matrix.config.bioc }}-${{ secrets.CACHE_VERSION || 1 }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-${{ matrix.config.bioc }}-${{ secrets.CACHE_VERSION || 1 }}- | |
| # The install_github() on remotes is to ensure system_requirements() supports 22.04 | |
| - name: Install r-lib/remotes | |
| run: | | |
| remotes::install_github("r-lib/remotes", force = TRUE) | |
| print(paste0("Remotes version: ", packageVersion("remotes"))) | |
| shell: Rscript {0} | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "${{ matrix.config.os }}"))') | |
| - name: Install dependencies | |
| run: | | |
| getOption('repos'); | |
| print(paste0("R_BIOC_VERSION: ", Sys.getenv("R_BIOC_VERSION"))); | |
| remotes::install_deps(dependencies = TRUE, upgrade = 'always') | |
| # See: https://stackoverflow.com/questions/77370659/error-failed-to-collect-lazy-table-caused-by-error-in-db-collect-using | |
| # TODO: Updating to BiocFileCache 2.10.1 should ultimately fix this. This manifests in SingleR | |
| if (Sys.getenv("R_BIOC_VERSION") < '3.18') { devtools::install_version("dbplyr", version = "2.3.4") } | |
| # TODO: this is to fix the as_cholmod_sparse' not provided by package 'Matrix' errors. This should ultimately be removed | |
| install.packages('Matrix', type = 'source', force = TRUE, repos = 'https://cran.wustl.edu/') | |
| install.packages('irlba', type = 'source', force = TRUE, repos = 'https://cran.wustl.edu/') | |
| install.packages("pkgdown") | |
| remotes::install_cran("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Verify SDA | |
| run: | | |
| which sda_static_linux | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc${{ matrix.config.bioc }}-results | |
| path: check | |
| - name: Install package | |
| if: github.ref == 'refs/heads/master' && matrix.config.pkgdown == 'true' | |
| run: R CMD INSTALL . | |
| - name: Deploy package | |
| if: github.ref == 'refs/heads/master' && matrix.config.pkgdown == 'true' | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Actions" | |
| Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, clean = TRUE)' |