update.packages {utils}R Documentation

Download Packages from CRAN-like repositories

Description

These functions can be used to automatically compare the version numbers of installed packages with the newest available version on the repositories and update outdated packages on the fly.

Usage

update.packages(lib.loc = NULL, repos = getOption("repos"),
                contriburl = contrib.url(repos, type),
                method, instlib = NULL,
                ask = TRUE, available = NULL,
                oldPkgs = NULL, ..., checkBuilt = FALSE,
                type = getOption("pkgType"))

available.packages(contriburl = contrib.url(getOption("repos"), type),
                   method, fields = NULL, type = getOption("pkgType"),
                   filters = NULL)

old.packages(lib.loc = NULL, repos = getOption("repos"),
             contriburl = contrib.url(repos, type),
             instPkgs = installed.packages(lib.loc = lib.loc),
             method, available = NULL, checkBuilt = FALSE,
             type = getOption("pkgType"))

new.packages(lib.loc = NULL, repos = getOption("repos"),
             contriburl = contrib.url(repos, type),
             instPkgs = installed.packages(lib.loc = lib.loc),
             method, available = NULL, ask = FALSE, ...,
             type = getOption("pkgType"))

download.packages(pkgs, destdir, available = NULL,
                  repos = getOption("repos"),
                  contriburl = contrib.url(repos, type),
                  method, type = getOption("pkgType"), ...)

install.packages(pkgs, lib, repos = getOption("repos"),
                 contriburl = contrib.url(repos, type),
                 method, available = NULL, destdir = NULL,
                 dependencies = NA, type = getOption("pkgType"),
                 configure.args = getOption("configure.args"),
                 configure.vars = getOption("configure.vars"),
                 clean = FALSE, Ncpus = getOption("Ncpus"), ...)

contrib.url(repos, type = getOption("pkgType"))

Arguments

lib.loc character vector describing the location of R library trees to search through (and update packages therein), or NULL for all known trees (see .libPaths).
repos character vector, the base URL(s) of the repositories to use, i.e., the URL of the CRAN master such as "http://cran.r-project.org" or its Statlib mirror, "http://lib.stat.cmu.edu/R/CRAN". Can be NULL to install from local files (‘.tar.gz’ for source packages).
contriburl URL(s) of the contrib sections of the repositories. Use this argument only if your repository mirror is incomplete, e.g., because you burned only the ‘contrib’ section on a CD. Overrides argument repos. As repos, can also be NULL to install from local files.
method Download method, see download.file.
pkgs character vector of the short names of packages/bundles whose current versions should be downloaded from the repositories. If repos = NULL, a character vector of file paths of ‘.tar.gz’ files. These can be source archives or binary package/bundle archive files (as created by R CMD build --binary). Tilde-expansion will be done on the file paths. If this is a zero-length character vector, a listbox of available packages (including those contained in bundles) is presented where possible.
destdir directory where downloaded packages are stored.
available an object listing packages available at the repositories as returned by available.packages.
lib character vector giving the library directories where to install the packages. Recycled as needed. If missing, defaults to .libPaths()[1].
ask logical indicating whether to ask user before packages are actually downloaded and installed, or the character string "graphics", which brings up a widget to allow the user to (de-)select from the list of packages which could be updated. The latter only works on systems with a GUI version of select.list, and is otherwise equivalent to ask = TRUE.
checkBuilt If TRUE, a package built under an earlier minor version of R is considered to be ‘old’.
instlib character string giving the library directory where to install the packages.
dependencies logical indicating to also install uninstalled packages on which these packages depend/suggest/import (and so on recursively). Not used if repos = NULL. Can also be a character vector, a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances").

Only supported if lib is of length one (or missing), so it is unambiguous where to install the dependent packages.

The default, NA, means c("Depends", "Imports", "LinkingTo") if lib is unambiguous, and FALSE otherwise.

configure.args (not Windows) a character vector or a named list. If a character vector with no names is supplied, the elements are concatenated into a single string (separated by a space) and used as the value for the --configure-args flag in the call to R CMD INSTALL. If the character vector has names these are assumed to identify values for --configure-args for individual packages. This allows one to specify settings for an entire collection of packages which will be used if any of those packages are to be installed. (These settings can therefore be reused and act as default settings.)

A named list can be used also to the same effect, and that allows multi-element character strings for each package which are concatenated to a single string to be used as the value for --configure-args.

configure.vars (not Windows) similar, for --configure-vars, which is used to set environment variables for the configure run.
oldPkgs if specified as non-NULL, update.packages() only considers these packages for updating.
instPkgs by default all installed packages, installed.packages(lib.loc=lib.loc). A subset can be specified; currently this must be in the same (character matrix) format as returned by installed.packages().
... (for update.packages). Arguments such as destdir, installWithVers and dependencies to be passed to install.packages.

(for new.packages). Arguments such as destdir and dependencies to be passed to install.packages.

(for install.packages and download.packages) arguments to be passed to download.file.

type character, indicating the type of package to download and install.

Possible values except on Windowsare "source" (the default except under the CRAN Mac OS X build), "mac.binary" and "win.binary" (which can be downloaded but not installed).

Possible values on Windows are "win.binary" (the default) and "source" (for which suitable tools may need to be installed: see the ‘Details’). Value "mac.binary" can be used to explore and download Mac OS X binaries.

clean a logical value indicating whether to specify to add the --clean flag to the call to R CMD INSTALL. This is sometimes used to perform additional operations at the end of the package installation in addition to removing intermediate files.
Ncpus The number of parallel processes to use for a parallel install of source packages. Values greater than one are supported only if GNU make is in use (more precisely, if make -j Ncpus works). Defaults to 1 is the option is unset.
fields a character vector giving the fields to extract from the PACKAGES file(s) in addition to the default ones, or NULL (default). Unavailable fields result in NA values.
filters a character vector or list specifying the filter operations to be performed on the packages found in the repositories, or NULL (default). Specified filters can be one of the strings "R_version", "OS_type", "duplicates", or "license/FOSS", indicating built-in filters which retain only packages whose version and OS type requirements are met by the running version of R, the latest versions of packages, and packages for which installation can proceed solely based on packages which can be verified as Free or Open Source Software (FOSS, e.g., http://en.wikipedia.org/wiki/FOSS) employing the available license specifications, respectively. Filters can also be user-defined functions which subscript the rows of objects returned by available.packages. The default corresponds to the specification c("R_version", "OS_type", "duplicates"), and may be changed by setting option available_packages_filters to something non-NULL. If the filters specification used is a list with an add = TRUE element, the other elements are used for filtering in addition to the default filters.

Details

All of these functions work with the names of a package or bundle (and not the component packages of a bundle, except for install.packages if the repository provides the necessary information).

available.packages returns a matrix of details corresponding to packages/bundles currently available at one or more repositories. The current list of packages is downloaded over the internet (or copied from a local mirror). By default, it returns only packages whose version and OS type requirements are met by the running version of R, and only information on the latest versions or packages.

old.packages compares the information from available.packages with that from instPkgs (computed by installed.packages by default) and reports installed packages/bundles that have newer versions on the repositories or, if checkBuilt = TRUE, that were built under an earlier minor version of R (for example built under 2.8.x when running R 2.9.0).

new.packages does the same comparison but reports uninstalled packages/bundles that are available at the repositories. It will give warnings about incompletely installed bundles (provided the information is available) and bundles whose contents has changed. If ask != FALSE it asks which packages should be installed in the first element of lib.loc.

download.packages takes a list of package/bundle names and a destination directory, downloads the newest versions and saves them in destdir. If the list of available packages is not given as argument, it is obtained from repositories. If a repository is local, i.e. the URL starts with "file:", then the packages are not downloaded but used directly. Both "file:" and "file:///" are allowed as prefixes to a file path. Use the latter only for URLs: see url for their interpretation. (Other forms of file:// URLs are not supported.)

The main function of the set is update.packages. First a list of all packages/bundles found in lib.loc is created and compared with those available at the repositories. If ask = TRUE (the default) packages/bundles with a newer version are reported and for each one the user can specify if it should be updated. If so, the package sources are downloaded from the repositories and installed in the respective library path (or instlib if specified) using the R INSTALL mechanism.

install.packages can be used to install new packages/bundles. It takes a vector of names and a destination library, downloads the packages from the repositories and installs them. (If the library is omitted it defaults to the first directory in .libPaths(), with a warning if there is more than one.) If lib is omitted or is of length one and is not a (group) writeable directory, the code offers to create a personal library tree (the first element of Sys.getenv("R_LIBS_USER")) and install there.

If a repository is used (rather than local ‘.tar.gz’ files), an attempt is made to install the packages in an order that respects their dependencies. This does assume that all the entries in lib are on the default library path for installs (set by R_LIBS).

contrib.url adds the appropriate type-specific path within a repository to each URL in repos.

For install.packages, destdir is the directory to which packages will be downloaded. If it is NULL (the default) a directory downloaded_packages of the session temporary directory will be used (and the files will be deleted at the end of the session).

If repos or contriburl is a vector of length greater than one, the newest version of the package compatible with this version of R is fetched from the first repository on the list within which it is found.

Value

For available.packages, a matrix with one row per package/bundle, row names the package names and column names "Package", "Version", "Priority", "Bundle", "Contains", "Depends", "Imports", "LinkingTo", "Suggests", "Enhances", "OS_type", "License", "File" and "Repository". Additional columns can be specified using the fields argument.

For old.packages, NULL or a matrix with one row per package/bundle, row names the package names and column names "Package", "LibPath", "Installed" (the version), "Built" (the version built under), "ReposVer" and "Repository".

For new.packages a character vector of package/bundle names, after any have been installed.

For download.packages, a two-column matrix of names and destination file names, for those packages/bundles successfully downloaded. If packages are not available or there is a problem with the download, suitable warnings are given.

install.packages and update.packages have no return value.

Warning

Take care when using dependencies with update.packages, for it is unclear where new dependencies should be installed. The current implementation will only allow it if all the packages to be updated are in a single library, when that library will be used.

You are advised to run update.packages before install.packages to ensure that any installed dependencies have their latest versions.

Note

Some binary distributions of R have INSTALL in a separate bundle, e.g. an R-devel RPM. install.packages will give an error if called with type = "source" on such a system.

See Also

installed.packages, remove.packages

See download.file for how to handle proxies and other options to monitor file transfers.

INSTALL, REMOVE, library, .packages, read.dcf

The ‘R Installation and Administration’ manual for how to set up a repository.

Examples


## Not run: 
install.packages(
    c("XML_0.99-5.tar.gz",
      "../../Interfaces/Perl/RSPerl_0.8-0.tar.gz"),
    repos = NULL,
    configure.args = c(XML = '--with-xml-config=xml-config',
                       RSPerl = "--with-modules='IO Fcntl'"))

## End(Not run)

[Package utils version 2.10.1 Index]