clean slate (ff2ad163) · Commits · github_fork / Presto 20250701

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

deleted100644 → 0

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		on:
		push:
		branches:
		- '*'
		pull_request:
		branches:
		- '*'

		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: windows-latest, r: '4.1'}
		- {os: macOS-latest, r: '4.1'}
		- {os: macOS-latest, r: 'devel'}
		- {os: ubuntu-22.04, r: '4.1'}
		- {os: ubuntu-20.04, r: '4.1'}

		env:
		R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
		R_CHECK_FORCE_SUGGESTS: false
		RSPM: ${{ matrix.config.rspm }}

		steps:
		- uses: actions/checkout@v2

		- uses: r-lib/actions/setup-r@v2.3.0
		with:
		r-version: ${{ matrix.config.r }}
		use-public-rspm: true

		- uses: r-lib/actions/setup-pandoc@v2.3.0

		- name: Query dependencies
		run: \|
		install.packages('remotes')
		saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
		shell: Rscript {0}

		- name: Cache R packages
		if: runner.os != 'Windows'
		uses: actions/cache@v1
		with:
		path: ${{ env.R_LIBS_USER }}
		key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
		restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-

		- name: Install system dependencies
		if: runner.os == 'Linux'
		env:
		RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
		run: \|
		Rscript -e "remotes::install_github('r-hub/sysreqs')"
		sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
		sudo -s eval "$sysreqs"

		- name: Install dependencies
		run: \|
		remotes::install_deps(dependencies = TRUE)
		remotes::install_cran("rcmdcheck")
		shell: Rscript {0}

		- name: Session info
		run: \|
		sessionInfo()
		shell: Rscript {0}

		- name: Check
		run: \|
		rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
		shell: Rscript {0}

		- name: Upload check results
		if: failure()
		uses: actions/upload-artifact@master
		with:
		name: ${{ runner.os }}-r${{ matrix.config.r }}-results
		path: check

.gitignore

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		@@ -6,3 +6,5 @@ src/*.so
		src/*.o
		.ipynb_checkpoints
		**/.ipynb_checkpoints
		*.swp
		*.swo

CRAN-RELEASE

deleted100644 → 0

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		This package was submitted to CRAN on 2019-05-08.
		Once it is accepted, delete this file and tag the release (commit 0574596dd4).

DESCRIPTION

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		@@ -19,29 +19,22 @@ Description: Scalable implementation of the Wilcoxon rank sum test and auROC sta
		License: GPL-3
		LazyData: true
		Encoding: UTF-8
		Depends: R (>= 3.4.0), Rcpp, data.table
		Depends: R (>= 3.4.0), Rcpp
		LinkingTo: Rcpp, RcppArmadillo
		biocViews:
		Imports:
		dplyr,
		methods,
		tidyr,
		purrr,
		tibble,
		Matrix,
		rlang,
		stats,
		utils
		Seurat,
		SingleCellExperiment,
		SummarizedExperiment,
		magrittr,
		Matrix
		RoxygenNote: 7.2.1
		Suggests:
		knitr,
		rmarkdown,
		testthat,
		Seurat,
		SingleCellExperiment,
		SummarizedExperiment,
		broom,
		BiocStyle,
		DESeq2
		testthat
		NeedsCompilation: yes
		VignetteBuilder: knitr

NAMESPACE

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		# Generated by roxygen2: do not edit by hand

		S3method(nnzeroGroups,dgCMatrix)
		S3method(nnzeroGroups,matrix)
		S3method(rank_matrix,dgCMatrix)
		S3method(rank_matrix,matrix)
		S3method(sumGroups,dgCMatrix)
		S3method(sumGroups,matrix)
		S3method(wilcoxauc,Seurat)
		S3method(wilcoxauc,SingleCellExperiment)
		S3method(wilcoxauc,default)
		S3method(wilcoxauc,seurat)
		export("%>%")
		export(collapse_counts)
		export(compute_hash)
		export(nnzeroGroups)
		export(pseudobulk_deseq2)
		export(pseudobulk_one_vs_all)
		export(pseudobulk_pairwise)
		export(pseudobulk_within)
		export(rank_matrix)
		export(sumGroups)
		export(summarize_dge_pairs)
		export(top_markers)
		export(top_markers_dds)
		export(wilcoxauc)
		import(Rcpp)
		importClassesFrom(Matrix,TsparseMatrix)
		@@ -30,22 +11,10 @@ importClassesFrom(Matrix,dgCMatrix)
		importClassesFrom(Matrix,dgTMatrix)
		importClassesFrom(Matrix,dgeMatrix)
		importFrom(Matrix,Matrix)
		importFrom(Rcpp,evalCpp)
		importFrom(Rcpp,loadModule)
		importFrom(Rcpp,sourceCpp)
		importFrom(data.table,data.table)
		importFrom(dplyr,"%>%")
		importFrom(dplyr,arrange)
		importFrom(dplyr,mutate)
		importFrom(dplyr,select)
		importFrom(magrittr,"%>%")
		importFrom(methods,as)
		importFrom(methods,is)
		importFrom(purrr,reduce)
		importFrom(rlang,.data)
		importFrom(stats,as.formula)
		importFrom(stats,p.adjust)
		importFrom(stats,pnorm)
		importFrom(stats,wilcox.test)
		importFrom(tibble,rownames_to_column)
		importFrom(utils,head)
		useDynLib(presto)

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