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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;} </style> </head> <body data-spy="scroll" data-target="#toc"> <div class="container-fluid"> <div class="row"> <header class="col-sm-12 col-lg-3 sidebar sidebar-book"><a class="sr-only sr-only-focusable" href="#content">Skip to main content</a> <div class="d-flex align-items-start justify-content-between"> <h1> <a href="index.html" title="">Bioconductor Packages: Development, Maintenance, and Peer Review</a> </h1> <button class="btn btn-outline-primary d-lg-none ml-2 mt-1" type="button" data-toggle="collapse" data-target="#main-nav" aria-expanded="true" aria-controls="main-nav"><i class="fas fa-bars"></i><span class="sr-only">Show table of contents</span></button> </div> <div id="main-nav" class="collapse-lg"> <form role="search"> <input id="search" class="form-control" type="search" placeholder="Search" aria-label="Search"> </form> <nav aria-label="Table of contents"><h2>Table of contents</h2> <ul class="book-toc list-unstyled"> <li><a class="" href="index.html">Welcome</a></li> <li class="book-part">Package Submissions</li> <li><a class="" href="submission-overview.html">Overview</a></li> <li><a class="" href="bioconductor-package-submissions.html"><span class="header-section-number">1</span> Bioconductor Package Submissions</a></li> <li class="book-part">Package Development Guidelines</li> <li><a class="" href="develop-overview.html">Overview</a></li> <li><a class="" href="package-name.html"><span class="header-section-number">2</span> Package name</a></li> <li><a class="" href="general.html"><span class="header-section-number">3</span> General Bioconductor Package Development</a></li> <li><a class="" href="important-bioconductor-package-development-features.html"><span class="header-section-number">4</span> Important Bioconductor Package Development Features</a></li> <li><a class="" href="readme.html"><span class="header-section-number">5</span> The README file</a></li> <li><a class="" href="description.html"><span class="header-section-number">6</span> The DESCRIPTION file</a></li> <li><a class="" href="namespace.html"><span class="header-section-number">7</span> The NAMESPACE file</a></li> <li><a class="" href="news.html"><span class="header-section-number">8</span> The NEWS file</a></li> <li><a class="" href="license.html"><span class="header-section-number">9</span> The LICENSE file</a></li> <li><a class="" href="citation.html"><span class="header-section-number">10</span> The CITATION file</a></li> <li><a class="" href="sysdep.html"><span class="header-section-number">11</span> The INSTALL file</a></li> <li><a class="" href="docs.html"><span class="header-section-number">12</span> Documentation</a></li> <li><a class="" href="data.html"><span class="header-section-number">13</span> Package data</a></li> <li><a class="" href="tests.html"><span class="header-section-number">14</span> Unit tests</a></li> <li><a class="" href="r-code.html"><span class="header-section-number">15</span> R code</a></li> <li><a class="" href="other-than-Rcode.html"><span class="header-section-number">16</span> Fortran / C / C++ / Python / Third-Party Code</a></li> <li><a class="" href="shiny.html"><span class="header-section-number">17</span> Shiny apps</a></li> <li><a class="" href="non-software.html"><span class="header-section-number">18</span> Non-Software Packages</a></li> <li><a class="" href="gitignore.html"><span class="header-section-number">19</span> The .gitignore file</a></li> <li><a class="" href="conclusion.html"><span class="header-section-number">20</span> Conclusion</a></li> <li class="book-part">Bioconductor Package Maintenance</li> <li><a class="" href="package-maintenance.html">Overview</a></li> <li><a class="" href="git-version-control.html"><span class="header-section-number">21</span> Git Version Control</a></li> <li><a class="active" href="versionnum.html"><span class="header-section-number">22</span> Version Numbering</a></li> <li><a class="" href="troubleshooting-build-report.html"><span class="header-section-number">23</span> Troubleshooting Build Report</a></li> <li><a class="" href="debugging-cc-code.html"><span class="header-section-number">24</span> Debugging C/C++ code</a></li> <li><a class="" href="deprecation.html"><span class="header-section-number">25</span> Deprecation Guidelines</a></li> <li><a class="" href="package-end-of-life-policy.html"><span class="header-section-number">26</span> Package End of Life Policy</a></li> <li><a class="" href="branch-rename-faqs.html"><span class="header-section-number">27</span> Branch Rename FAQs</a></li> <li class="book-part">Package Reviewer Resources</li> <li><a class="" href="reviewer-resources-overview.html">Overview</a></li> <li><a class="" href="review-expectation.html"><span class="header-section-number">28</span> Review Expectations</a></li> <li><a class="" href="reviewtools.html"><span class="header-section-number">29</span> Reviewer Resources and Tools</a></li> <li><a class="" href="review-volunteer-chapter.html"><span class="header-section-number">30</span> Volunteer to Review</a></li> <li class="book-part">Appendix</li> <li><a class="" href="use-devel.html"><span class="header-section-number">A</span> Using the ‘Devel’ Version of Bioconductor</a></li> <li><a class="" href="long-tests.html"><span class="header-section-number">B</span> Long Tests</a></li> <li><a class="" href="querying-web-resources.html"><span class="header-section-number">C</span> Querying Web Resources</a></li> <li><a class="" href="c-fortran.html"><span class="header-section-number">D</span> C and Fortran code</a></li> <li><a class="" href="cmavericks-best-practices.html"><span class="header-section-number">E</span> C++/Mavericks Best Practices</a></li> <li><a class="" href="man-links.html"><span class="header-section-number">F</span> Debug: Links in Rd files</a></li> <li><a class="" href="booknews.html"><span class="header-section-number">G</span> NEWS</a></li> </ul> <div class="book-extra"> <p><a id="book-repo" href="https://github.com/Bioconductor/pkgrevdocs">View book source <i class="fab fa-github"></i></a></p> </div> </nav> </div> </header><main class="col-sm-12 col-md-9 col-lg-7" id="content"><div id="versionnum" class="section level1" number="22"> <h1> <span class="header-section-number">22</span> Version Numbering<a class="anchor" aria-label="anchor" href="#versionnum"><i class="fas fa-link"></i></a> </h1> <p>All <em>Bioconductor</em> packages should have a version number in x.y.z format.</p> <p>Examples of good version numbers:</p> <pre><code>1.2.3 0.99.5 2.3.0 3.12.44</code></pre> <div id="even-odd-schedule" class="section level2" number="22.1"> <h2> <span class="header-section-number">22.1</span> Even Odd Schedule<a class="anchor" aria-label="anchor" href="#even-odd-schedule"><i class="fas fa-link"></i></a> </h2> <p><em>Bioconductor</em> has a ‘devel’ branch where new features are introduced, and release branches created twice per year. Given a package with version number x.y.z,</p> <ul> <li>y should be an odd number in devel.</li> <li>y should be an even number in release.</li> </ul> <p>During regular development of new features</p> <ul> <li>Authors increment the z version of their package in the ‘devel’ branch by 1 for each GIT commit, e.g., from 1.1.0 to 1.1.1, 1.1.2, …, 1.1.10, 1.1.11</li> <li>Any bug fixes ported to the release branch are similarly incremented, 1.0.1, 1.0.2, …</li> <li>Changes made to GIT without a corresponding version bump <strong>do not propagate</strong> to the repository visible to <code><a href="https://bioconductor.github.io/BiocManager/reference/install.html">BiocManager::install()</a></code>.</li> </ul> <p>At the time of a release, the <em>Bioconductor</em> team arranges to:</p> <ul> <li>Create a release branch package with version: x <strong>.</strong> (y+1) <strong>.</strong> (z-z)</li> <li>Increment the devel branch package version to: x <strong>.</strong> (y+2) <strong>.</strong> (z-z)</li> <li>As a special case, any package with version x.99.z is bumped to (x+1) <strong>.</strong> 0 <strong>.</strong> (z-z) in release, and (x+1) <strong>.</strong> 1 <strong>.</strong> 0 in devel. Thus authors wishing to signify a major change to their package should set y to 99 in their devel package.</li> </ul> </div> <div id="new-packages" class="section level2" number="22.2"> <h2> <span class="header-section-number">22.2</span> New packages<a class="anchor" aria-label="anchor" href="#new-packages"><i class="fas fa-link"></i></a> </h2> <p>New packages submitted to <em>Bioconductor</em> should set Version: 0.99.0 in the DESCRIPTION file. Specifying y=99 triggers a bump in x at the next release which in this case results in version 1.0.0.</p> <p>See additional details on the <a href="bioconductor-package-submissions.html#subintro">Package Submission</a> page.</p> <p>See also the instructions for <a href="use-devel.html#use-devel">Using Bioc Devel</a>.</p> </div> <div id="example-cases" class="section level2" number="22.3"> <h2> <span class="header-section-number">22.3</span> Example Cases<a class="anchor" aria-label="anchor" href="#example-cases"><i class="fas fa-link"></i></a> </h2> <ol style="list-style-type: decimal"> <li><p>Normal Case. Suppose a package in the devel branch has version number 1.1.25. The new release branch now contains a copy of the package with version 1.2.0. The devel branch of <em>Bioconductor</em> contains the package whose version number has been bumped to 1.3.0</p></li> <li><p>Special Case. The “0.99.2” version of our package is copied by the <em>Bioconductor</em> team to the release branch with version number 1.0.0. The package version is bumped to 1.1.0 in the devel branch.</p></li> </ol> <p>Examples of the version bumping scheme:</p> <div class="inline-table"><table border="1" cellpadding="5" cellspacing="0" class="table table-sm"> <thead valign="bottom"><tr> <th class="head"> Current Release </th> <th class="head"> Current Devel </th> <th class="head"> Just before Next release </th> <th class="head"> Next release </th> <th class="head"> Next devel </th> </tr></thead> <tbody valign="top"> <tr> <td> – </td> <td> 0.99.1 </td> <td> 0.99.2 </td> <td> 1.0.0 </td> <td> 1.1.0 </td> </tr> <tr> <td> 1.4.0 </td> <td> 1.5.0 </td> <td> 1.5.4 </td> <td> 1.6.0 </td> <td> 1.7.0 </td> </tr> <tr> <td> 1.4.0 </td> <td> 1.5.0 </td> <td> 1.5.1 </td> <td> 1.6.0 </td> <td> 1.7.0 </td> </tr> <tr> <td> 1.4.0 </td> <td> 1.5.0 </td> <td> 1.99.3 </td> <td> 2.0.0 </td> <td> 2.1.0 </td> </tr> <tr> <td> 1.8.0 </td> <td> 1.9.0 </td> <td> 1.9.1 </td> <td> 1.10.0 </td> <td> 1.11.0 </td> </tr> </tbody> </table></div> <p><br></p> </div> <div id="summary" class="section level2" number="22.4"> <h2> <span class="header-section-number">22.4</span> Summary<a class="anchor" aria-label="anchor" href="#summary"><i class="fas fa-link"></i></a> </h2> <p>Below is a summary of how version components are bumped and the key limitations. Bumps “at release time” are done by the <em>Bioconductor</em> team and not the package maintainer.</p> <p><code>x</code> - only modified by the <em>Bioconductor</em> team - bumped to x+1 at release time if y=99 <code>y</code> - must be even in release and odd in devel - must be <=99 - bumped at release time for all packages to the next even number in release and the next odd in devel <code>z</code> - should be incremented sequentially during regular package development - no limitation on the size of z - bumped at release time to 0 for all packages.</p> </div> </div> <div class="chapter-nav"> <div class="prev"><a href="git-version-control.html"><span class="header-section-number">21</span> Git Version Control</a></div> <div class="next"><a href="troubleshooting-build-report.html"><span class="header-section-number">23</span> Troubleshooting Build Report</a></div> </div></main><div class="col-md-3 col-lg-2 d-none d-md-block sidebar sidebar-chapter"> <nav id="toc" data-toggle="toc" aria-label="On this page"><h2>On this page</h2> <ul class="nav navbar-nav"> <li><a class="nav-link" href="#versionnum"><span class="header-section-number">22</span> Version Numbering</a></li> <li><a class="nav-link" href="#even-odd-schedule"><span class="header-section-number">22.1</span> Even Odd Schedule</a></li> <li><a class="nav-link" href="#new-packages"><span class="header-section-number">22.2</span> New packages</a></li> <li><a class="nav-link" href="#example-cases"><span class="header-section-number">22.3</span> Example Cases</a></li> <li><a class="nav-link" href="#summary"><span class="header-section-number">22.4</span> Summary</a></li> </ul> <div class="book-extra"> <ul class="list-unstyled"> <li><a id="book-source" href="https://github.com/Bioconductor/pkgrevdocs/blob/devel/version-numbering.Rmd">View source <i class="fab fa-github"></i></a></li> <li><a id="book-edit" href="https://github.com/Bioconductor/pkgrevdocs/edit/devel/version-numbering.Rmd">Edit this page <i class="fab fa-github"></i></a></li> </ul> </div> </nav> </div> </div> </div>  <footer class="bg-primary text-light mt-5"><div class="container"><div class="row"> <div class="col-12 col-md-6 mt-3"> <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2025-02-24.</p> </div> <div class="col-12 col-md-6 mt-3"> <p>This book was built by the <a class="text-light" href="https://bookdown.org">bookdown</a> R package.</p> </div> </div></div> </footer><script> (function () { var script = document.createElement("script"); script.type = "text/javascript"; var src = "true"; if (src === "" || src === "true") src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/latest.js?config=TeX-MML-AM_CHTML"; if (location.protocol !== "file:") if (/^https?:/.test(src)) src = src.replace(/^https?:/, ''); script.src = src; document.getElementsByTagName("head")[0].appendChild(script); })(); </script><script type="text/x-mathjax-config">const popovers = document.querySelectorAll('a.footnote-ref[data-toggle="popover"]'); for (let popover of popovers) { const div = document.createElement('div'); div.setAttribute('style', 'position: absolute; top: 0, left:0; width:0, height:0, overflow: hidden; visibility: hidden;'); div.innerHTML = popover.getAttribute('data-content'); var has_math = div.querySelector("span.math"); if (has_math) { document.body.appendChild(div); MathJax.Hub.Queue(["Typeset", MathJax.Hub, div]); MathJax.Hub.Queue(function() { popover.setAttribute('data-content', div.innerHTML); document.body.removeChild(div); }) } } </script> </body> </html>