\HeaderA{update.packages}{Download Packages from CRAN-like repositories}{update.packages}
\aliasA{available.packages}{update.packages}{available.packages}
\aliasA{contrib.url}{update.packages}{contrib.url}
\aliasA{download.packages}{update.packages}{download.packages}
\aliasA{install.packages}{update.packages}{install.packages}
\aliasA{new.packages}{update.packages}{new.packages}
\aliasA{old.packages}{update.packages}{old.packages}
\keyword{utilities}{update.packages}
\begin{Description}\relax
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the repositories and update outdated packages on the fly.
\end{Description}
\begin{Usage}
\begin{verbatim}
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")),
                   method, fields = NULL)

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

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,
                 installWithVers = FALSE, dependencies = NA,
                 type = getOption("pkgType"),
                 configure.args = character(0),
                 clean = FALSE, ...)

contrib.url(repos, type = getOption("pkgType"))
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{lib.loc}] character vector describing the location of R
library trees to search through (and update packages therein).
\item[\code{repos}] character vector, the base URL(s) of the repositories
to use, i.e., the URL of the CRAN master such as
\code{"http://cran.r-project.org"} or its Statlib mirror,
\code{"http://lib.stat.cmu.edu/R/CRAN"}.
Can be \code{NULL} to install from local files
(\file{.tar.gz} for source packages).

\item[\code{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 \file{contrib} section on a
CD.  Overrides argument \code{repos}.
As \code{repos}, can also be \code{NULL} to install from local files.

\item[\code{method}] Download method, see \code{\LinkA{download.file}{download.file}}.
\item[\code{pkgs}] character vector of the short names of packages/bundles whose
current versions should be downloaded from the repositories.
If \code{repos = NULL}, a character vector of file paths of
\file{.tar.gz} files.  These can be source archives or binary
package/bundle archive files (as created by \code{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.

\item[\code{destdir}] directory where downloaded packages are stored.
\item[\code{available}] an object listing packages available at the repositories
as returned by \code{available.packages}.
\item[\code{lib}] character vector giving the library directories where to
install the packages.  Recycled as needed.  If missing, defaults to
\code{\LinkA{.libPaths}{.libPaths}()[1]}.
\item[\code{ask}] logical indicating whether to ask user before packages
are actually downloaded and installed, or the character string
\code{"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
\code{\LinkA{select.list}{select.list}}, and is otherwise equivalent to \code{ask
      = TRUE}.

\item[\code{installWithVers}] If \code{TRUE}, will invoke the install of the
package such that it can be referenced by package version.
\item[\code{checkBuilt}] If \code{TRUE}, a package built under an earlier
minor version of \R{} is considered to be \sQuote{old}.
\item[\code{instlib}] character string giving the library directory where to
install the packages.
\item[\code{dependencies}] logical indicating to also install uninstalled
packages on which these packages depend/suggest/import
(and so on recursively).  Not used if \code{repos = NULL}.
Can also be a character vector, a subset of
\code{c("Depends", "Imports", "Suggests")}.  Note that only if the
dependent package is \emph{installed} is checked, not if it meets
the version requirements.

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

The default, \code{NA}, means \code{c("Depends", "Imports")} if
\code{lib} is unambiguous, and \code{FALSE} otherwise.

\item[\code{configure.args}] 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 \code{--configure-args}
flag in the call to \code{R CMD INSTALL}.
If the character vector has names, these are assumed to identify
values for \code{--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 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 \code{--configure-args}.

\item[\code{oldPkgs}] if specified as non-NULL, \code{update.packages()} only considers
these packages for updating. 

\item[\code{instPkgs}] by default all installed packages,
\code{\LinkA{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 \code{installed.packages()}.

\item[\code{...}] (for \code{update.packages}).  Arguments such as \code{destdir},
\code{installWithVers} and \code{dependencies} to be passed to
\code{install.packages}.

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

(for \code{install.packages} and \code{download.packages}) arguments
to be passed to \code{\LinkA{download.file}{download.file}}.

\item[\code{type}] character, indicating the type of package to download and
install.
Possible values are \code{"source"} (the default except under the
CRAN Mac OS X build), \code{"mac.binary"} and \code{"win.binary"}
(which can be downloaded but not installed).

\item[\code{clean}] a logical value indicating whether to specify
to add the \code{--clean} flag to the call to \code{R CMD INSTALL}.
This is sometimes used to perform additional operations at the end
of the package installation in addition to removing intermediate files.

\item[\code{fields}] a character vector giving the fields to extract from
the \code{PACKAGES} file(s) in addition to the default ones, or
\code{NULL} (default).  Unavailable fields result in \code{NA}
values.

\end{ldescription}
\end{Arguments}
\begin{Details}\relax
All of these functions work with the names of a package or bundle (and
not the component packages of a bundle, except for
\code{install.packages} if the repository provides the necessary
information).

\code{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).  It returns only packages whose version
requirements are met by the running version of \R.

\code{old.packages} compares the information from
\code{available.packages} with that from \code{instPkgs}
(\code{\LinkA{installed.packages}{installed.packages}} by default) and reports installed
packages/bundles that have newer versions on the repositories or, if
\code{checkBuilt = TRUE}, that were built under an earlier minor
version of \R{} (for example built under 2.0.x when running \R{} 2.1.1).

\code{new.packages} does the same comparison but reports uninstalled
packages/bundles that are available at the repositories.  (It checks
the front-end package \pkg{gnomeGUI} separately.)  It will
give warnings about incompletely installed bundles (provided the
information is available) and bundles whose contents has changed.
If \code{ask != FALSE} it asks which packages should be installed
in the first element of \code{lib.loc}.  NB: versioned installs are
not installs of a named package.

\code{download.packages} takes a list of package/bundle names and a
destination directory, downloads the newest versions and saves them in
\code{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 \code{"file:"}, then the packages are not
downloaded but used directly.  Both \code{"file:"} and
\code{"file:///"} are allowed as prefixes to a file path.  Use the
latter only for URLs: see \code{\LinkA{url}{url}} for their interpretation.
(Other forms of \code{"file://"} URLs are not supported.)

The main function of the set is \code{update.packages}.  First a list
of all packages/bundles found in \code{lib.loc} is created and
compared with those available at the repositories.  If \code{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 \code{instlib}
if specified) using the \R{} \code{\LinkA{INSTALL}{INSTALL}} mechanism.

\code{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 \code{.libPaths()}, with a warning if there is more than one.)  If
\code{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 \code{Sys.getenv("R\_LIBS\_USER")}) and install
there.

If a repository is used (rather than local \file{.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
\code{lib} are on the default library path for installs (set by
\code{R\_LIBS}). 

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

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

If \code{repos} or \code{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.
\end{Details}
\begin{Value}
For \code{available.packages}, a matrix
with one row per package/bundle, row names the package names and
column names \code{"Package"}, \code{"Version"}, \code{"Priority"},
\code{"Bundle"}, \code{"Depends"}, \code{"Imports"}, \code{"Suggests"}
\code{"Contains"} and \code{"Repository"}.  Additional columns can
be specified using the \code{fields} argument.

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

For \code{new.packages} a character vector of package/bundle names,
\emph{after} any have been installed.

For \code{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.

\code{install.packages} and \code{update.packages} have no return value.
\end{Value}
\begin{Section}{Warning}
Take care when using \code{dependencies} with \code{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 \code{update.packages} before
\code{install.packages} to ensure that any installed dependencies have
their latest versions.
\end{Section}
\begin{Note}\relax
Some binary distributions of \R{} have \code{INSTALL} in a separate
bundle, e.g. an \code{R-devel} RPM.  \code{install.packages} will
give an error if called on such a system.
\end{Note}
\begin{SeeAlso}\relax
\code{\LinkA{installed.packages}{installed.packages}}, \code{\LinkA{remove.packages}{remove.packages}}

See \code{\LinkA{download.file}{download.file}} for how to handle proxies and
other options to monitor file transfers.

\code{\LinkA{INSTALL}{INSTALL}}, \code{\LinkA{REMOVE}{REMOVE}},
\code{\LinkA{library}{library}}, \code{\LinkA{.packages}{.packages}}, \code{\LinkA{read.dcf}{read.dcf}}

The \sQuote{R Installation and Administration} manual for how to 
set up a repository.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

## 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)
\end{ExampleCode}
\end{Examples}

