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<div id="welcome-to-rcy3-2-0-and-beyond" class="section level1">
<div class="page-header"><h1 class="hasAnchor">
<a href="#welcome-to-rcy3-2-0-and-beyond" class="anchor"></a>Welcome to RCy3: 2.0 and Beyond</h1></div>
<p>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:</p>
<ul>
<li>independence from the graphNEL object model</li>
<li>harmonized function and argument names</li>
<li>support for Cytoscape commands</li>
<li>better support for Cytoscape apps</li>
<li>see <a href="https://github.com/cytoscape/RCy3/blob/master/NEWS">NEWS</a> for the complete release notes</li>
<li>coordinated development with CyREST and the Cytoscape service model
<ul>
<li><a href="https://github.com/cytoscape/cyREST/issues?utf8=%E2%9C%93&q=milestone%3A*+label%3A%22new+API%22+is%3A*">New API</a></li>
</ul>
</li>
<li>coordinated development with other scripting libraries, e.g.,
<ul>
<li><a href="https://github.com/cytoscape/py2cytoscape">py2cytoscape</a></li>
<li><a href="http://bioconductor.org/packages/release/bioc/html/RCyjs.html">RCyjs</a></li>
</ul>
</li>
</ul>
<div id="getting-started" class="section level2">
<h2 class="hasAnchor">
<a href="#getting-started" class="anchor"></a>Getting Started</h2>
<ul>
<li><a href="http://cytoscape.org/RCy3/index.html">Documenation site</a></li>
<li><a href="https://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/">Cytoscape Rmd noteboods</a></li>
</ul>
</div>
<div id="how-to-install" class="section level2">
<h2 class="hasAnchor">
<a href="#how-to-install" class="anchor"></a>How to install</h2>
<p><strong><em>Official bioconductor releases</em> (recommended)</strong></p>
<pre><code><a href="https://rdrr.io/r/utils/install.packages.html">install.packages("BiocManager")
BiocManager::install("RCy3")</a></code></pre>
<p><em>Development version from this repo</em> (at your own risk)</p>
<pre><code><a href="https://rdrr.io/r/utils/install.packages.html">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)</a></code></pre>
<div id="troubleshooting" class="section level4">
<h4 class="hasAnchor">
<a href="#troubleshooting" class="anchor"></a>Troubleshooting</h4>
<ol>
<li>If you see this error on a Mac: <code>make: gfortran-4.8: No such file or directory</code>, then try reinstalling R via <a href="https://brew.sh/">homebrew</a>: <code>brew update && brew reinstall r</code>
<ul>
<li>warning: this may take ~30 minutes</li>
</ul>
</li>
<li>If you see this error in RStudio: <code>ERROR: dependency ‘XML’ is not available for package</code>, then try this command: <code><a href="https://rdrr.io/r/utils/install.packages.html">install.packages("XML")</a></code> and then try installing RCy3 again.</li>
</ol>
</div>
</div>
<div id="how-to-contribute" class="section level2">
<h2 class="hasAnchor">
<a href="#how-to-contribute" class="anchor"></a>How to contribute</h2>
<p>This is a public, open source project. Come on in! You can contribute at multiple levels:</p>
<ul>
<li>Report an issue or feature request</li>
<li>Fork and make pull requests</li>
<li>Contact current Cytoscape developers and inquire about joining the team</li>
</ul>
<div id="development" class="section level3">
<h3 class="hasAnchor">
<a href="#development" class="anchor"></a>Development</h3>
<pre><code><a href="https://rdrr.io/r/utils/install.packages.html">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('./')</a></code></pre>
</div>
<div id="testing" class="section level3">
<h3 class="hasAnchor">
<a href="#testing" class="anchor"></a>Testing</h3>
<p>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):</p>
<pre><code><a href="https://rdrr.io/r/base/source.html">source(system.file("unitTests", "test_RCy3.R", package="RCy3"))
run.tests()</a></code></pre>
<p>They take about 4 minutes to run.</p>
</div>
<div id="updating-site" class="section level3">
<h3 class="hasAnchor">
<a href="#updating-site" class="anchor"></a>Updating site</h3>
<p>We use <a href="https://pkgdown.r-lib.org/">pkgdown</a> to generate the <a href="http://cytoscape.org/RCy3/index.html">main site for RCy3</a> 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:</p>
<pre><code><a href="https://rdrr.io/r/base/library.html">library(pkgdown)
pkgdown::build_site()</a></code></pre>
</div>
<div id="bioconductor" class="section level3">
<h3 class="hasAnchor">
<a href="#bioconductor" class="anchor"></a>Bioconductor</h3>
<p>While this is the primary development repository for the RCy3 project, we also make regular pushes to official bioconductor repository (<a href="http://bioconductor.org/packages/devel/bioc/html/RCy3.html">devel</a> & <a href="http://bioconductor.org/packages/release/bioc/html/RCy3.html">release</a>) 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 <code>master</code> branch here corresponds to the latest code in development and not yet released.</p>
<pre><code>git commit -m "informative commit message"
git push origin master
git push upstream master</code></pre>
<p><a href="http://bioconductor.org/developers/how-to/git/push-to-github-bioc/" class="uri">http://bioconductor.org/developers/how-to/git/push-to-github-bioc/</a></p>
<p>Following each bioconductor release, a <code>RELEASE_#_#</code> branch is created here:</p>
<pre><code>git fetch upstream
git checkout -b RELEASE_3_10 upstream/RELEASE_3_10
git push origin RELEASE_3_10</code></pre>
<p>Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to <code>master</code>, then:</p>
<pre><code>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</code></pre>
<p><a href="https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/" class="uri">https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/</a></p>
</div>
<div id="vignettes" class="section level3">
<h3 class="hasAnchor">
<a href="#vignettes" class="anchor"></a>Vignettes</h3>
<p>When adding or updating vignettes, consider the following tips for consistency:</p>
<ul>
<li>Copy/paste the header from an existing RCy3 vignette, including the global knitr options</li>
<li>Number the <em>VignetteIndexEntry</em> names w.r.t. other vignettes (this determines their presentation order)</li>
<li>Avoid spaces in Rmd filenames; causes CHECK errors</li>
<li>When ready, run <strong>Knit to html_document</strong> and review the generated html (requires BiocStyle)</li>
<li>Note: you don’t need to save the html version; it will be generated anew at Bioconductor.</li>
<li>In the end, you should just have an Rmd version of each vignette in the repo.</li>
</ul>
</div>
<div id="former-repo" class="section level3">
<h3 class="hasAnchor">
<a href="#former-repo" class="anchor"></a>Former Repo</h3>
<p>The entire commit history has been preserved during this transition, but you can find the repo for RCy3 v1.5.3 and earlier at <a href="https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape" class="uri">https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape</a> and you can find the Bioconductor page for v1.8.0, including archives at <a href="https://www.bioconductor.org/packages/3.6/bioc/html/RCy3.html" class="uri">https://www.bioconductor.org/packages/3.6/bioc/html/RCy3.html</a>.</p>
<p><code>Note to repository maintainers: Please *DO NOT* move this page ... the Cytoscape Automation paper refers directly to it.</code></p>
</div>
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<h2>Links</h2>
<ul class="list-unstyled">
<li>Download from BIOC at <br><a href="https://www.bioconductor.org/packages/RCy3">https://www.bioconductor.org/packages/RCy3</a>
</li>
<li>Browse source code at <br><a href="https://github.com/cytoscape/RCy3">https://github.com/cytoscape/RCy3</a>
</li>
<li>Report a bug at <br><a href="https://github.com/cytoscape/RCy3/issues">https://github.com/cytoscape/RCy3/issues</a>
</li>
</ul>
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<div class="license">
<h2>License</h2>
<ul class="list-unstyled">
<li>
<a href="https://opensource.org/licenses/mit-license.php">MIT</a> + file <a href="LICENSE-text.html">LICENSE</a>
</li>
</ul>
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<h2>Citation</h2>
<ul class="list-unstyled">
<li><a href="authors.html">Citing RCy3</a></li>
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<div class="developers">
<h2>Developers</h2>
<ul class="list-unstyled">
<li>Alex Pico <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-5706-2163" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
<li>Tanja Muetze <br><small class="roles"> Author </small> </li>
<li>Paul Shannon <br><small class="roles"> Author </small> </li>
<li><a href="authors.html">All authors...</a></li>
</ul>
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<h2>Dev status</h2>
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<li><a href="https://travis-ci.org/cytoscape/RCy3"><img src="https://travis-ci.org/cytoscape/RCy3.svg?branch=master" alt="Travis-CI Build Status"></a></li>
</ul>
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<p>Developed by Alex Pico, Tanja Muetze, Paul Shannon.</p>
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