Building upon the phenominal success of RCytoscape and RCy3, Cytoscape is adopting this project to provide a robust R package for the rapidly evolving Cytoscape ecosystem. We are beginning with a major refactor of RCy3 that includes:
Official bioconductor releases (recommended)
Development version from this repo (at your own risk)
install.packages("devtools") library(devtools) install_github('cytoscape/RCy3', build_vignettes=TRUE) #If installation fails due to package 'XXX' not found, # then run install.packages("XXX") and then try install_github('cytoscape/RCy3') again library(RCy3)
make: gfortran-4.8: No such file or directory, then try reinstalling R via homebrew:
brew update && brew reinstall r
ERROR: dependency ‘XML’ is not available for package, then try this command:
install.packages("XML")and then try installing RCy3 again.
This is a public, open source project. Come on in! You can contribute at multiple levels:
install.packages("devtools") install.packages("roxygen2") library(devtools,roxygen2) devtools::install_github("AlexanderPico/docthis") library(docthis) #shift+cmd+D BiocManager::install("BiocStyle") library(BiocStyle) BiocManager::install("BiocCheck") library(BiocCheck) install.packages("RUnit") library(RUnit) setwd("/git/cytoscape/RCy3") #customize to your setup devtools::document() devtools::check() BiocCheck::BiocCheck('./')
Unit tests are a crucial tool in software development. In order to run them ‘offline’ (not on the Bioconductor build system), take these steps from within a running R session (requires RUnit):
They take about 4 minutes to run.
While this is the primary development repository for the RCy3 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
master branch here corresponds to the latest code in development and not yet released.
git commit -m "informative commit message" git push origin master git push upstream master
Following each bioconductor release, a
RELEASE_#_# branch is created here:
git fetch upstream git checkout -b RELEASE_3_10 upstream/RELEASE_3_10 git push origin RELEASE_3_10
Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to
git checkout RELEASE_3_10 git cherry-pick master #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_10 # double check changes, and then... git push upstream RELEASE_3_10 git checkout master # bump dev version in DESCRIPTION git commit -am 'version bump' git push origin master git push upstream master
When adding or updating vignettes, consider the following tips for consistency:
The entire commit history has been preserved during this transition, but you can find the repo for RCy3 v1.5.3 and earlier at https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape and you can find the Bioconductor page for v1.8.0, including archives at https://www.bioconductor.org/packages/3.6/bioc/html/RCy3.html.
Note to repository maintainers: Please *DO NOT* move this page ... the Cytoscape Automation paper refers directly to it.