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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>R: Install a development package from the Bioconductor git...</title> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <link rel="stylesheet" type="text/css" href="R.css" /> </head><body> <table width="100%" summary="page for install_bioc {remotes}"><tr><td>install_bioc {remotes}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Install a development package from the Bioconductor git repository</h2> <h3>Description</h3> <p>This function requires <code>git</code> to be installed on your system in order to be used. </p> <h3>Usage</h3> <pre> install_bioc( repo, mirror = getOption("BioC_git", download_url("git.bioconductor.org/packages")), git = c("auto", "git2r", "external"), dependencies = NA, upgrade = c("default", "ask", "always", "never"), force = FALSE, quiet = FALSE, build = TRUE, build_opts = c("--no-resave-data", "--no-manual", "--no-build-vignettes"), build_manual = FALSE, build_vignettes = FALSE, repos = getOption("repos"), type = getOption("pkgType"), ... ) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>repo</code></td> <td> <p>Repository address in the format <code style="white-space: pre;">[username:password@][release/]repo[#commit]</code>. Valid values for the release are ‘devel’, ‘release’ (the default if none specified), or numeric release numbers (e.g. ‘3.3’).</p> </td></tr> <tr valign="top"><td><code>mirror</code></td> <td> <p>The Bioconductor git mirror to use</p> </td></tr> <tr valign="top"><td><code>git</code></td> <td> <p>Whether to use the <code>git2r</code> package, or an external git client via system. Default is <code>git2r</code> if it is installed, otherwise an external git installation.</p> </td></tr> <tr valign="top"><td><code>dependencies</code></td> <td> <p>Which dependencies do you want to check? Can be a character vector (selecting from "Depends", "Imports", "LinkingTo", "Suggests", or "Enhances"), or a logical vector. </p> <p><code>TRUE</code> is shorthand for "Depends", "Imports", "LinkingTo" and "Suggests". <code>NA</code> is shorthand for "Depends", "Imports" and "LinkingTo" and is the default. <code>FALSE</code> is shorthand for no dependencies (i.e. just check this package, not its dependencies). </p> <p>The value "soft" means the same as <code>TRUE</code>, "hard" means the same as <code>NA</code>. </p> <p>You can also specify dependencies from one or more additional fields, common ones include: </p> <ul> <li><p> Config/Needs/website - for dependencies used in building the pkgdown site. </p> </li> <li><p> Config/Needs/coverage for dependencies used in calculating test coverage. </p> </li></ul> </td></tr> <tr valign="top"><td><code>upgrade</code></td> <td> <p>Should package dependencies be upgraded? One of "default", "ask", "always", or "never". "default" respects the value of the <code>R_REMOTES_UPGRADE</code> environment variable if set, and falls back to "ask" if unset. "ask" prompts the user for which out of date packages to upgrade. For non-interactive sessions "ask" is equivalent to "always". <code>TRUE</code> and <code>FALSE</code> are also accepted and correspond to "always" and "never" respectively.</p> </td></tr> <tr valign="top"><td><code>force</code></td> <td> <p>Force installation, even if the remote state has not changed since the previous install.</p> </td></tr> <tr valign="top"><td><code>quiet</code></td> <td> <p>If <code>TRUE</code>, suppress output.</p> </td></tr> <tr valign="top"><td><code>build</code></td> <td> <p>If <code>TRUE</code> build the package before installing.</p> </td></tr> <tr valign="top"><td><code>build_opts</code></td> <td> <p>Options to pass to <code style="white-space: pre;">R CMD build</code>, only used when <code>build</code> is <code>TRUE</code>.</p> </td></tr> <tr valign="top"><td><code>build_manual</code></td> <td> <p>If <code>FALSE</code>, don't build PDF manual ('–no-manual').</p> </td></tr> <tr valign="top"><td><code>build_vignettes</code></td> <td> <p>If <code>FALSE</code>, don't build package vignettes ('–no-build-vignettes').</p> </td></tr> <tr valign="top"><td><code>repos</code></td> <td> <p>A character vector giving repositories to use.</p> </td></tr> <tr valign="top"><td><code>type</code></td> <td> <p>Type of package to <code>update</code>.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Other arguments passed on to <code><a href="../../utils/html/install.packages.html">utils::install.packages()</a></code>.</p> </td></tr> </table> <h3>Details</h3> <p>It is vectorised so you can install multiple packages with a single command. </p> <p>This is intended as an aid for Bioconductor developers. If you want to install the release version of a Bioconductor package one can use the <code>BiocManager</code> package. </p> <h3>See Also</h3> <p>Other package installation: <code><a href="install_bitbucket.html">install_bitbucket</a>()</code>, <code><a href="install_cran.html">install_cran</a>()</code>, <code><a href="install_dev.html">install_dev</a>()</code>, <code><a href="install_github.html">install_github</a>()</code>, <code><a href="install_gitlab.html">install_gitlab</a>()</code>, <code><a href="install_git.html">install_git</a>()</code>, <code><a href="install_local.html">install_local</a>()</code>, <code><a href="install_svn.html">install_svn</a>()</code>, <code><a href="install_url.html">install_url</a>()</code>, <code><a href="install_version.html">install_version</a>()</code> </p> <h3>Examples</h3> <pre> ## Not run: install_bioc("SummarizedExperiment") install_bioc("devel/SummarizedExperiment") install_bioc("3.3/SummarizedExperiment") install_bioc("SummarizedExperiment#abc123") install_bioc("user:password@release/SummarizedExperiment") install_bioc("user:password@devel/SummarizedExperiment") install_bioc("user:password@SummarizedExperiment#abc123") ## End(Not run) </pre> <hr /><div style="text-align: center;">[Package <em>remotes</em> version 2.4.2 <a href="00Index.html">Index</a>]</div> </body></html>