try modified R-CMD-check.yaml (982f6006) · Commits · github_fork / DTUrtle

.github/workflows/R-CMD-check.yaml

+7 −5

Original line number	Diff line number	Diff line
		@@ -27,7 +27,6 @@ jobs:
		R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
		GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
		R_KEEP_PKG_SOURCE: yes
		UPGRADE_PKGS: ${{ matrix.config.r == '3.6' }}

		steps:
		- uses: actions/checkout@v2
		@@ -51,15 +50,18 @@ jobs:
		# set Bioc Goettingen mirror
		options("BioC_mirror"="https://ftp.gwdg.de/pub/misc/bioconductor")
		BiocManager::install(c("BiocParallel", "GenomicRanges", "Gviz", "rtracklayer", "stageR", "tximport", "DESeq2", "GenomicFeatures", "glmGamPoi", "apeglm", "GenomeInfoDb"))
		remotes::install_deps(dependencies = TRUE)
		remotes::install_deps(dependencies = TRUE, upgrade="never")
		remotes::install_cran("rcmdcheck")
		shell: Rscript {0}

		- name: glmGamPoi and Seurat for R < 4.0
		if: runner.os == "Linux" && ${{ env.UPGRADE_PKGS }}
		if: matrix.config.r == '3.6'
		run: \|
		remotes::install_github("const-ae/glmGamPoi")
		remotes::install_version("Seurat", version="3.0.0")
		# set Bioc Goettingen mirror
		options("BioC_mirror"="https://ftp.gwdg.de/pub/misc/bioconductor")
		BiocManager::install("multtest", upgrade="never")
		remotes::install_github("const-ae/glmGamPoi", upgrade="never")
		remotes::install_version("Seurat", version="3.0.0", upgrade="never")
		shell: Rscript {0}

		- uses: r-lib/actions/check-r-package@v1