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# R Client Package for WikiPathways [![BioC Release Build Status](]( - Bioconductor Release Build [![BioC Dev Build Status](]( - Bioconductor Dev Build R Client library for the WikiPathways API ( (license: MIT). WikiPathays is described in the following papers: * 2016 NAR paper by [Kutmon et al.]( * 2018 NAR paper by [Slenter et al.](https://doi.or/10.1093/nar/gkx1064) * 2021 NAR paper by [Martens et al.]( If you like this package, or want to make it easier to work with Xrefs, then you may also like these R packages: * [BridgeDbR]( * [PathVisioRPC]( * [RCy3]( ## Getting Started * [Documentation site]( * [Overview vignette](articles/Overview.html) ## How to install **_Official bioconductor releases_ (recommended)** ``` if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("rWikiPathways") ``` *Note: Be sure to use the [latest Bioconductor]( and recommended R version* **_Unstable development code from this repo_ (at your own risk)** ``` install.packages("devtools") library(devtools) install_github('wikipathways/rWikiPathways', build_vignettes=TRUE) library(rWikiPathways) ``` #### Troubleshooting 1. If you see this error on a Mac: ```make: gfortran-4.8: No such file or directory```, then try reinstalling R via [homebrew]( ```brew update && brew reinstall r``` * warning: this make take ~30 minutes ## How to contribute This is a public, open source project. Come on in! You can contribute at multiple levels: * Report an issue or feature request * Fork and make pull requests * Contact current WikiPathways developers and inquire about joining the team ### Development ``` install.packages("devtools") install.packages("roxygen2") library(devtools,roxygen2) devtools::install_github("AlexanderPico/docthis") library(docthis) setwd("/git/wikipathways/rWikiPathways") #customize to your setup devtools::document() devtools::check(vignettes = F) BiocCheck::BiocCheck('./') ``` ### Testing Unit tests are a crucial tool in software development. Be sure to [add tests](tests/testthat) for any new methods implemented. These will be run as part of the `devtools::check()`. ### Updating site We use [pkgdown]( to generate the [main site for rWikiPathways]( based on this README, metadata, man pages and vignettes. If you make changes to any of these, please take a moment to regenerate the site: ``` library(pkgdown) pkgdown::build_site() ``` ### Bioconductor While this is the primary development repository for the rWikiPathways project, we also make regular pushes to official bioconductor repository ([devel]( & [release]( from which the official releases are generated. This is the correct repo for all coding and bug reporting interests. The tagged releases here correspond to the bioconductor releases via a manual syncing process. The `devel` branch here corresponds to the latest code in development and not yet released. ``` git commit -m "informative commit message" git push origin devel git push upstream devel ``` Following each bioconductor release, a `RELEASE_#_#` branch is created. The new branch is fetched and devel is updated: ``` git fetch upstream git checkout -b RELEASE_3_15 upstream/RELEASE_3_15 git push origin RELEASE_3_15 git checkout devel git pull upstream devel git push origin devel ``` Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `devel`, then: ``` git checkout RELEASE_3_15 git cherry-pick devel #for lastest commit # or git cherry-pick 1abc234 #for specific commit # or git cherry-pick 1abc234^..5def678 #for an inclusive range # bump release version in DESCRIPTION git commit -am 'version bump' git push origin RELEASE_3_15 # double check changes, and then... git push upstream RELEASE_3_15 git checkout devel # bump dev version in DESCRIPTION git commit -am 'version bump' git push origin devel git push upstream devel ``` And then finally, bump version and commit DESCRIPTION to `devel` and push to origin and upstream. ### Vignettes When adding or updating vignettes, consider the following tips for consistency: * Copy/paste the header from an existing rWikiPathways vignette, including the global knitr options * Number the *VignetteIndexEntry* names w.r.t. other vignettes (this determines their presentation order) * Avoid spaces in Rmd filenames; causes CHECK errors * When ready, run **Knit to html_vignette_** and review the generated html * Note: you don't need to save the html version; it will be generated anew at Bioconductor. * In the end, you should just have an Rmd version of each vignette in the repo.