diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..91114bf --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,2 @@ +^.*\.Rproj$ +^\.Rproj\.user$ diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml new file mode 100644 index 0000000..34df233 --- /dev/null +++ b/.github/workflows/rworkflows.yml @@ -0,0 +1,57 @@ +name: rworkflows +'on': + push: + branches: + - master + - main + - devel + - RELEASE_** + pull_request: + branches: + - master + - main + - devel + - RELEASE_** +jobs: + rworkflows: + permissions: + contents: write + runs-on: ${{ matrix.config.os }} + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + container: ${{ matrix.config.cont }} + strategy: + fail-fast: ${{ false }} + matrix: + config: + - os: ubuntu-latest + bioc: devel + r: auto + cont: bioconductor/bioconductor_docker:devel + rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release + - os: macOS-latest + bioc: release + r: auto + cont: ~ + rspm: ~ + - os: windows-latest + bioc: release + r: auto + cont: ~ + rspm: ~ + steps: + - uses: neurogenomics/rworkflows@master + with: + run_bioccheck: ${{ false }} + run_rcmdcheck: ${{ true }} + as_cran: ${{ true }} + run_vignettes: ${{ true }} + has_testthat: ${{ true }} + run_covr: ${{ true }} + run_pkgdown: ${{ true }} + has_runit: ${{ false }} + has_latex: ${{ false }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run_docker: ${{ false }} + DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} + runner_os: ${{ runner.os }} + cache_version: cache-v1 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..cbae048 --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +.Rproj.user +.Rhistory +.RData +.Ruserdata +*.RProj diff --git a/DESCRIPTION b/DESCRIPTION index 6632124..fc9d0ba 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: GenomicFiles Title: Distributed computing by file or by range Description: This package provides infrastructure for parallel - computations distributed 'by file' or 'by range'. User + computations distributed 'by file' or 'by range'. User- defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation. Version: 1.37.0 @@ -33,6 +33,7 @@ Collate: GenomicFiles-class.R unpack-methods.R registry.R zzz.R +URL: https://github.com/Bioconductor/GenomicFiles Video: https://www.youtube.com/watch?v=3PK_jx44QTs RoxygenNote: 6.1.0 VignetteBuilder: knitr diff --git a/README.Rmd b/README.Rmd new file mode 100644 index 0000000..3de8418 --- /dev/null +++ b/README.Rmd @@ -0,0 +1,41 @@ +--- +title: "`r read.dcf('DESCRIPTION', fields = 'Package')[1]`" +author: "`r rworkflows::use_badges()`" +date: "

README updated: `r format( Sys.Date(), '%b-%d-%Y')`

" +output: + github_document +--- + + + +```{r, echo=FALSE, include=FALSE} +pkg <- read.dcf("DESCRIPTION", fields = "Package")[1] +title <- read.dcf("DESCRIPTION", fields = "Title")[1] +description <- read.dcf("DESCRIPTION", fields = "Description")[1] +URL <- read.dcf('DESCRIPTION', fields = 'URL')[1] +owner <- tolower(strsplit(URL,"/")[[1]][4]) +``` + +## ``r pkg``: `r title` + +### `r gsub("\n","",description)` + +If you use ``r pkg``, please cite: + + +> `r utils::citation(pkg)$textVersion` + +## Installation + +```R +if (!require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") + +BiocManager::install("`r pkg`") +``` +## Documentation + +### [Website](https://`r owner`.github.io/`r pkg`) +### [Get started](https://`r owner`.github.io/`r pkg`/articles/`r pkg`) + +
diff --git a/README.md b/README.md index b25013b..edaf964 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,45 @@ GenomicFiles -========= +================ +NULL [![License: +Artistic-2.0](https://img.shields.io/badge/license-Artistic--2.0-blue.svg)](https://cran.r-project.org/web/licenses/Artistic-2.0) +[![](https://img.shields.io/badge/devel%20version-1.37.0-black.svg)](https://github.com/Bioconductor/GenomicFiles) +[![](https://img.shields.io/github/languages/code-size/Bioconductor/GenomicFiles.svg)](https://github.com/Bioconductor/GenomicFiles) +[![](https://img.shields.io/github/last-commit/Bioconductor/GenomicFiles.svg)](https://github.com/Bioconductor/GenomicFiles/commits/master) +
[![R build +status](https://github.com/Bioconductor/GenomicFiles/workflows/rworkflows/badge.svg)](https://github.com/Bioconductor/GenomicFiles/actions) +[![](https://codecov.io/gh/Bioconductor/GenomicFiles/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Bioconductor/GenomicFiles) +
+ +

+Authors: +

+

+README updated: Sep-01-2023 +

-Distributed computing by file or by range + +## `GenomicFiles`: Distributed computing by file or by range + +### This package provides infrastructure for parallelcomputations distributed ‘by file’ or ‘by range’. User-defined MAPPER and REDUCER functions provide addedflexibility for data combination and manipulation. + +If you use `GenomicFiles`, please cite: + + + +## Installation + +``` r +if (!require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") + +BiocManager::install("GenomicFiles") +``` + +## Documentation + +### [Website](https://bioconductor.github.io/GenomicFiles) + +### [Get started](https://bioconductor.github.io/GenomicFiles/articles/GenomicFiles) + +