From d35f7a1fbf80be851ee4357ff000b7df7d9ebe43 Mon Sep 17 00:00:00 2001 From: Maria Doyle Date: Fri, 27 May 2022 18:11:35 +0100 Subject: [PATCH 1/2] Update github action to Bioc 3.15 --- .github/workflows/check-bioc.yml | 48 ++++++++++---------------------- 1 file changed, 14 insertions(+), 34 deletions(-) diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 71e74fe5..f6011a9f 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -39,7 +39,6 @@ env: run_pkgdown: 'true' has_RUnit: 'false' cache-version: 'cache-v1' - run_docker: 'false' jobs: build-check: @@ -52,9 +51,9 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:RELEASE_3_14", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } - - { os: macOS-latest, r: '4.1', bioc: '3.14'} - - { os: windows-latest, r: '4.1', bioc: '3.14'} + - { os: ubuntu-latest, r: '4.2', bioc: '3.15', cont: "bioconductor/bioconductor_docker:RELEASE_3_15", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } + - { os: macOS-latest, r: '4.2', bioc: '3.15'} + - { os: windows-latest, r: '4.2', bioc: '3.15'} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} @@ -102,16 +101,16 @@ jobs: uses: actions/cache@v2 with: path: ${{ env.R_LIBS_USER }} - key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1- + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2- - name: Cache R packages on Linux if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " uses: actions/cache@v2 with: path: /home/runner/work/_temp/Library - key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1- + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2- - name: Install Linux system dependencies if: runner.os == 'Linux' @@ -157,13 +156,6 @@ jobs: run: | BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) shell: Rscript {0} - - ## 12th April 2021 No Seurat binary available for Mac currently so install from source - - name: Install Seurat for macOS-latest - if: matrix.config.os == 'macOS-latest' - run: | - BiocManager::install("Seurat", type="source") - shell: Rscript {0} - name: Install dependencies pass 1 run: | @@ -173,9 +165,6 @@ jobs: ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html ## https://github.com/r-lib/remotes/issues/296 ## Ideally, all dependencies should get installed in the first pass. - - ## To fix preprocessCore error https://github.com/stemangiola/tidybulk/issues/145 - BiocManager::install("preprocessCore", configure.args="--disable-threading") ## Pass #1 at installing dependencies message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) @@ -188,7 +177,7 @@ jobs: ## Pass #2 at installing dependencies message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE) - + ## For running the checks message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) remotes::install_cran("rcmdcheck") @@ -211,7 +200,7 @@ jobs: - name: Install pkgdown if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' run: | - remotes::install_github("r-lib/pkgdown") + remotes::install_cran("pkgdown") shell: Rscript {0} - name: Session info @@ -250,9 +239,7 @@ jobs: dir('check', 'tar.gz$', full.names = TRUE), `quit-with-status` = TRUE, `no-check-R-ver` = TRUE, - `no-check-bioc-help` = TRUE, - `no-check-library-calls` = TRUE, - `no-check-coding-practices` = TRUE + `no-check-bioc-help` = TRUE ) shell: Rscript {0} @@ -269,6 +256,9 @@ jobs: - name: Deploy package if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' run: | + ## Temporary workaround for https://github.com/actions/checkout/issues/766 + git config --global --add safe.directory "$GITHUB_WORKSPACE" + git config --local user.email "actions@github.com" git config --local user.name "GitHub Actions" Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)" @@ -282,15 +272,5 @@ jobs: if: failure() uses: actions/upload-artifact@master with: - name: ${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-results + name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results path: check - - - uses: docker/build-push-action@v1 - if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' " - with: - username: ${{ secrets.DOCKER_USERNAME }} - password: ${{ secrets.DOCKER_PASSWORD }} - repository: stemangiola/tidybulk - tag_with_ref: true - tag_with_sha: true - tags: latest From 4a110fa5bb44c1c9fd2cb25f4554708ab66843ec Mon Sep 17 00:00:00 2001 From: Maria Doyle Date: Sat, 28 May 2022 19:51:58 +0100 Subject: [PATCH 2/2] Edit to action --- .github/workflows/check-bioc.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index f6011a9f..989adb7d 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -239,7 +239,9 @@ jobs: dir('check', 'tar.gz$', full.names = TRUE), `quit-with-status` = TRUE, `no-check-R-ver` = TRUE, - `no-check-bioc-help` = TRUE + `no-check-bioc-help` = TRUE, + `no-check-library-calls` = TRUE, + `no-check-coding-practices` = TRUE ) shell: Rscript {0}