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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="" 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="active" 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="package-end-of-life-policy" class="section level1" number="26"> <h1> <span class="header-section-number">26</span> Package End of Life Policy<a class="anchor" aria-label="anchor" href="#package-end-of-life-policy"><i class="fas fa-link"></i></a> </h1> <p>The Bioconductor project strives to provide a software repository that is stable and relevant to users across the community. Each year about 100-150 new software packages are added to the repository; as of Spring 2021 over 2000 packages are hosted. The Bioconductor Build System (BBS) installs, builds, and checks each software package every 24 hours. Regular execution of example, vignette, and unit test code ensures the package is operating as expected and all required dependencies are available. The <a href="https://bioconductor.org/checkResults/">build system</a> provides a detailed report for each package across three platforms: Linux, Windows, and Mac.</p> <p>In an effort to maintain a high quality repository we have adopted a one-year end of life (EOL) process for packages that no longer pass build or check and do not have an active maintainer. Packages are assessed for EOL deprecation prior to each Bioconductor release; the EOL policies apply to software, annotation, workflow, and experiment data packages.</p> <div id="criteria-for-package-deprecation-by-core-team" class="section level2" number="26.1"> <h2> <span class="header-section-number">26.1</span> Criteria for package deprecation by Core Team<a class="anchor" aria-label="anchor" href="#criteria-for-package-deprecation-by-core-team"><i class="fas fa-link"></i></a> </h2> <ol style="list-style-type: decimal"> <li> <p>R CMD build or check errors on one or more platforms</p> <p>The package must build and check without error on all platforms (exceptions to cross-platform builds are available under limited circumstances) at each Bioconductor release. All efforts will be made to keep a package in the repository if the maintainer is actively attempting a fix.</p> <p>If a package is broken for an extended period of time the maintainer will be given a final 2 week notice. If the package is not fixed by the end of the 2 weeks, End of Life will be started.</p> </li> <li> <p>Inactive maintainer</p> <p>The maintainer listed in the DESCRIPTION file must be responsive to questions on the support site, package-related email from users and Bioconductor team members, package-related errors in the build system, and requests for bug fixes. The email in the DESCRIPTION must also remain a valid, active email.</p> </li> </ol> </div> <div id="user-requested-deprecation" class="section level2" number="26.2"> <h2> <span class="header-section-number">26.2</span> User Requested Deprecation<a class="anchor" aria-label="anchor" href="#user-requested-deprecation"><i class="fas fa-link"></i></a> </h2> <p>Alternatively, a package maintainer may request package deprecation. The maintainer may have any number of reasons for deprecating their package. Some common reasons include:</p> <ol style="list-style-type: decimal"> <li><p>They no longer wish to maintain their package</p></li> <li><p>The package functionality has been superseded by other packages</p></li> <li><p>The package material has become out-of-date and it makes sense to retire the package.</p></li> <li><p>Significant changes to the underlying technology e.g., a web API, have made the package unmaintainable.</p></li> </ol> <p>We ask that maintainers wishing to deprecate their package send an email notification to <a href="https://stat.ethz.ch/mailman/listinfo/bioc-devel">bioc-devel</a> mailing list. The core team will ensure all necessary steps and notifications can occur.</p> </div> <div id="end-of-life-process" class="section level2" number="26.3"> <h2> <span class="header-section-number">26.3</span> End of Life process<a class="anchor" aria-label="anchor" href="#end-of-life-process"><i class="fas fa-link"></i></a> </h2> <p><strong>Step I</strong>: Deprecation</p> <p>Packages to be deprecated will be marked with a deprecation warning and the package name will have a strikethrough on the build report. The warning is emitted when the package is loaded, and is reported on the package ‘landing page’. The message alerts users that the package currently fails the minimal build and check criteria, and that the package will likely be removed from Bioconductor in the next release.</p> <p>If at any time in this 6 month period the required criteria are met (e.g., the package returns to active maintenance, perhaps after ‘adoption’ by a third party) the warning is removed.</p> <p><strong>Step II</strong>: Defunct</p> <p>When a package has gone through one development cycle as ‘deprecated’ without remedial action, the package is marked as ‘Defunct’. The package is removed from the nightly build system, is no longer available through ‘BiocManager::install()’, and does not have a current ‘landing page’.</p> <p>The package remains available in the git archive, and in previous versions of Bioconductor.</p> <p>Defunct packages cannot re-enter the Bioconductor repository except through review as a ‘new package’.</p> <p><strong>Example</strong>:</p> <p>A package identified for deprecation during Bioconductor release 3.2 / devel 3.3 would make the following transitions:</p> <pre><code>- deprecate in devel 3.3 ** Bioc Release ** - deprecate in release 3.3 (i.e., no change in release status) - defunct in devel 3.4 ** Bioc Release ** - defunct in release 3.4 - gone in devel 3.5 ** Bioc Release ** - gone in release 3.5</code></pre> </div> <div id="implementation-detail" class="section level2" number="26.4"> <h2> <span class="header-section-number">26.4</span> Implementation detail<a class="anchor" aria-label="anchor" href="#implementation-detail"><i class="fas fa-link"></i></a> </h2> <ol style="list-style-type: decimal"> <li><p>Notify the bioc-devel mailing list and maintainers of packages Depending, Importing, or Suggesting the package that the package will be deprecated. If appropriate, indicate that a new maintainer is welcome to take over.</p></li> <li> <p>Add the following code chunk to the ‘devel’ version of the package in a file <code>R/zzz.R</code>, adjusting the Bioconductor version to the version <em>after</em> the current devel version.</p> <pre><code>.onAttach <- function(libname, pkgname) { msg <- sprintf( "Package '%s' is deprecated and will be removed from Bioconductor version %s", pkgname, "3.4") .Deprecated(msg=paste(strwrap(msg, exdent=2), collapse="\n")) }</code></pre> </li> <li> <p>Add the following annotation to the package DESCRIPTION file.</p> <p>PackageStatus: Deprecated</p> </li> <li><p>The package remains deprecated in the ‘devel’ branch for up to 6 months, after which time Bioconductor core team members remove the package from the ‘devel’ package manifest.</p></li> </ol> </div> <div id="reversing-end-of-life-status" class="section level2" number="26.5"> <h2> <span class="header-section-number">26.5</span> Reversing End of Life Status<a class="anchor" aria-label="anchor" href="#reversing-end-of-life-status"><i class="fas fa-link"></i></a> </h2> <p>A deprecated package can be un-deprecated and removed from the End of Life process if it is fixed before the next Bioconductor release. To have a package un-deprecated, please contact <a href="mailto:maintainer@bioconductor.org" class="email">maintainer@bioconductor.org</a>. If a package is already in the defunct stage; the package will mostly likely be requested to go through the new package submission process again.</p> </div> <div id="orphaned-packages" class="section level2" number="26.6"> <h2> <span class="header-section-number">26.6</span> ‘Orphaned’ packages<a class="anchor" aria-label="anchor" href="#orphaned-packages"><i class="fas fa-link"></i></a> </h2> <p>An ‘orphaned’ package is a Bioconductor package with an inactive and non-responsive maintainer. As described above, Bioconductor makes multiple efforts to reach out to package maintainers to fix broken packages. If there is no response from a maintainer to the emails sent out from the core team, the package is considered ‘orphaned’. Occasionally, members of the Bioconductor community reach out to take over maintenance of an ‘orphaned’ package. The interested replacement maintainer is asked to email the original maintainer and <a href="mailto:maintainer@bioconductor.org" class="email">maintainer@bioconductor.org</a>, to formally request permission to take over. Unless there is an explicit request for a package to be retired, Bioconductor will grant access to the interested replacement maintainer in accordance with open source software licenses that Bioconductor packages require and <a href="bioconductor-package-submissions.html#naming">package naming policy</a> that maintainers agree to upon submission.</p> </div> </div> <div class="chapter-nav"> <div class="prev"><a href="deprecation.html"><span class="header-section-number">25</span> Deprecation Guidelines</a></div> <div class="next"><a href="branch-rename-faqs.html"><span class="header-section-number">27</span> Branch Rename FAQs</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="#package-end-of-life-policy"><span class="header-section-number">26</span> Package End of Life Policy</a></li> <li><a class="nav-link" href="#criteria-for-package-deprecation-by-core-team"><span class="header-section-number">26.1</span> Criteria for package deprecation by Core Team</a></li> <li><a class="nav-link" href="#user-requested-deprecation"><span class="header-section-number">26.2</span> User Requested Deprecation</a></li> <li><a class="nav-link" href="#end-of-life-process"><span class="header-section-number">26.3</span> End of Life process</a></li> <li><a class="nav-link" href="#implementation-detail"><span class="header-section-number">26.4</span> Implementation detail</a></li> <li><a class="nav-link" href="#reversing-end-of-life-status"><span class="header-section-number">26.5</span> Reversing End of Life Status</a></li> <li><a class="nav-link" href="#orphaned-packages"><span class="header-section-number">26.6</span> ‘Orphaned’ packages</a></li> </ul> <div class="book-extra"> <ul class="list-unstyled"> <li><a id="book-source" href="https://github.com/Bioconductor/pkgrevdocs/blob/devel/package-end-of-life.Rmd">View source <i class="fab fa-github"></i></a></li> <li><a id="book-edit" href="https://github.com/Bioconductor/pkgrevdocs/edit/devel/package-end-of-life.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 2024-12-02.</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>