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description.html

@@ -265,7 +265,8 @@ <h2>
 be included to document the process. If a user facing <a href="readme.html#readme"><code>README</code></a> is included it
 is also recommended to document the process there; do not try to install a
 dependency for a user anywhere in the package (i.e. readme, r code, man pages,
-vignette). You may show instructions only in unevaluated sections.</p>
+vignette). You may show instructions only in unevaluated sections. See also
+<a href="r-code.html#rcode-sysdep">Additional files and dependencies</a></p>
 </div>
 <div id="description-biocviews" class="section level2" number="6.10">
 <h2>

r-code.html

@@ -329,16 +329,28 @@ <h4>
 <h4>
 <span class="header-section-number">15.2.6.5</span> Additional files and dependencies<a class="anchor" aria-label="anchor" href="#rcode-sysdep"><i class="fas fa-link"></i></a>
 </h4>
-<p>Do NOT install anything on a users system.</p>
-<p>System dependencies, applications, and additionally needed packages should be
-assumed already present on the user’s system.</p>
-<p>If necessary, package maintainers should provide instructions for download and
-setup, but should not execute those instructions on behalf of a
-user. Complicated or additional system dependency instructions could be part of
-the <a href="readme.html#readme">README file</a> and/or <a href="sysdep.html#sysdep">INSTALL file</a>. All package
-dependencies must actively be on CRAN or <a href="https://bioconductor.org"><em>Bioconductor</em></a>.</p>
+<p>Do NOT install anything on a users system! System dependencies, applications,
+and additionally needed packages should be assumed already present on the user’s
+system.</p>
+<p>Direct calls to external commands via
+system() or system2() are not ideal so should only be used when there is no
+other alternative. For example, if a CRAN or Bioconductor package already
+provides the functionality that you are after, you should use that instead.</p>
+<p>Now if your package <strong>absolutely</strong> must rely on external software then you
+need to make sure that those requirements are listed in
+the SystemRequirements field of the DESCRIPTION file of the package. These
+requirements should be “reasonable” requirements, that is, trusted software
+only, open source, and relatively easy to install.</p>
+<p>Additionally we ask that the package contains an <a href="sysdep.html#sysdep">INSTALL file</a> (in the
+top-level folder) that provides instructions for installing the external
+software on the 3 major OS that we support: Linux, Windows, and Mac. This
+will not only help your users get the external software on their machines,
+but it will also help us install it on the build machines if it’s not
+already there.</p>
 <p>All system and package dependencies should be the latest publically available
-version.</p>
+version. All package dependencies must actively be on CRAN or
+Bioconductor. Bioconductor will not recognize Remotes in Description and will
+not install a lower version of a package or dependency.</p>
 </div>
 <div id="rcode-namespaces" class="section level4" number="15.2.6.6">
 <h4>

sysdep.html

@@ -106,8 +106,11 @@ <h1>
 <p>An INSTALL file does not have to be included with the package. An INSTALL file
 is utilized for specifying external system requirements needed. It should be
 used in combination with the <code>SystemRequirements</code> field of the <a href="description.html#description-sysdep">Description
-file</a>. This file should contain installation instructions
-for the required system dependency.</p>
+file</a>. This file should provide instructions for installing
+the external software on the 3 major OS that we support: Linux, Windows, and
+Mac. This will not only help your users get the external software on their
+machines, but it will also help us install it on the build machines if it’s not
+already there.</p>
 <p>Specifying this requirement does not guarantee that <em>Bioconductor</em> will agree to
 install the external system requirement. It is encouraged to discuss any
 additional system requirements on the <a href="mailto:[email protected]" class="email">[email protected]</a> before