CINXE.COM

<!DOCTYPE html> <html lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <title>Chapter 7 The NAMESPACE file | Bioconductor Packages: Development, Maintenance, and Peer Review</title> <meta name="author" content="Kevin Rue-Albrecht"> <meta name="author" content="Daniela Cassol"> <meta name="author" content="Johannes Rainer"> <meta name="author" content="Lori Shepherd"> <meta name="description" content="A NAMESPACE file defines the functions, classes, and methods that are imported into the namespace, and exported for users. In the following section we describe what Bioconductor reviewers will be..."> <meta name="generator" content="bookdown 0.42 with bs4_book()"> <meta property="og:title" content="Chapter 7 The NAMESPACE file | Bioconductor Packages: Development, Maintenance, and Peer Review"> <meta property="og:type" content="book"> <meta property="og:description" content="A NAMESPACE file defines the functions, classes, and methods that are imported into the namespace, and exported for users. In the following section we describe what Bioconductor reviewers will be..."> <meta name="twitter:card" content="summary"> <meta name="twitter:title" content="Chapter 7 The NAMESPACE file | Bioconductor Packages: Development, Maintenance, and Peer Review"> <meta name="twitter:description" content="A NAMESPACE file defines the functions, classes, and methods that are imported into the namespace, and exported for users. In the following section we describe what Bioconductor reviewers will be..."> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://kit.fontawesome.com/6ecbd6c532.js" crossorigin="anonymous"></script><script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <link href="libs/bootstrap-4.6.0/bootstrap.min.css" rel="stylesheet"> <script src="libs/bootstrap-4.6.0/bootstrap.bundle.min.js"></script><script src="libs/bs3compat-0.9.0/transition.js"></script><script src="libs/bs3compat-0.9.0/tabs.js"></script><script src="libs/bs3compat-0.9.0/bs3compat.js"></script><link href="libs/bs4_book-1.0.0/bs4_book.css" rel="stylesheet"> <script src="libs/bs4_book-1.0.0/bs4_book.js"></script><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/all.min.css" integrity="sha512-9usAa10IRO0HhonpyAIVpjrylPvoDwiPUiKdWk5t3PyolY1cOd4DSE0Ga+ri4AuTroPR5aQvXU9xC6qOPnzFeg==" crossorigin="anonymous" referrerpolicy="no-referrer"> <script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><style type="text/css"> 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="active" 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="" 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="namespace" class="section level1" number="7"> <h1> <span class="header-section-number">7</span> The NAMESPACE file<a class="anchor" aria-label="anchor" href="#namespace"><i class="fas fa-link"></i></a> </h1> <p>A <a href="http://cran.fhcrc.org/doc/manuals/R-exts.html#Package-namespaces">NAMESPACE</a> file defines the functions, classes, and methods that are imported into the namespace, and exported for users.</p> <p>In the following section we describe what <a href="https://bioconductor.org"><em>Bioconductor</em></a> reviewers will be looking for in this file.</p> <div id="function-names" class="section level2" number="7.1"> <h2> <span class="header-section-number">7.1</span> Function names<a class="anchor" aria-label="anchor" href="#function-names"><i class="fas fa-link"></i></a> </h2> <p>Exported functions should use camel case or underscoring and not include <code>.</code>, which indicates S3 dispatch. Functions starting with <code>.</code> should not be exported as that indicates an internal function.</p> </div> <div id="imported-functions" class="section level2" number="7.2"> <h2> <span class="header-section-number">7.2</span> Imported functions<a class="anchor" aria-label="anchor" href="#imported-functions"><i class="fas fa-link"></i></a> </h2> <p>Generally <code>importFrom()</code> is encouraged over importing an entire package. However, if there are many functions from a single package, <code>import()</code> can be acceptable. If a particular <em>Bioconductor</em> class is used or extended it is highly recommended to <code>import()</code> the full package so that full class functionality is inherited automatically; there are exceptions depending on implementation and necessity.</p> </div> <div id="exported-functions" class="section level2" number="7.3"> <h2> <span class="header-section-number">7.3</span> Exported functions<a class="anchor" aria-label="anchor" href="#exported-functions"><i class="fas fa-link"></i></a> </h2> <p>Exporting all functions with <code>exportPattern("^[[:alpha:]]+")</code> is strongly discouraged and almost always not allowed. Functions and generics should be exported individually, for clarity and control.</p> </div> </div> <div class="chapter-nav"> <div class="prev"><a href="description.html"><span class="header-section-number">6</span> The DESCRIPTION file</a></div> <div class="next"><a href="news.html"><span class="header-section-number">8</span> The NEWS file</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="#namespace"><span class="header-section-number">7</span> The NAMESPACE file</a></li> <li><a class="nav-link" href="#function-names"><span class="header-section-number">7.1</span> Function names</a></li> <li><a class="nav-link" href="#imported-functions"><span class="header-section-number">7.2</span> Imported functions</a></li> <li><a class="nav-link" href="#exported-functions"><span class="header-section-number">7.3</span> Exported functions</a></li> </ul> <div class="book-extra"> <ul class="list-unstyled"> <li><a id="book-source" href="https://github.com/Bioconductor/pkgrevdocs/blob/devel/namespace-file.Rmd">View source <i class="fab fa-github"></i></a></li> <li><a id="book-edit" href="https://github.com/Bioconductor/pkgrevdocs/edit/devel/namespace-file.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>