R: Install Packages from Repositories or Local Files

install.packages {utils}

R Documentation

Install Packages from Repositories or Local Files

Description

Download and install packages from CRAN-like repositories or from local files.

Usage

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", 1L),
                 verbose = getOption("verbose"),
                 libs_only = FALSE, INSTALL_opts, quiet = FALSE,
                 keep_outputs = FALSE, ...)

Arguments

`pkgs`	character vector of the names of packages whose current versions should be downloaded from the repositories. If `repos = NULL`, a character vector of file paths. These can be source directories or archives or binary package archive files (as created by `R CMD build --binary`). (`http://` and `file://` URLs are also accepted and the files will be downloaded and installed from local copies.) On a CRAN build of R for OS X these can be ‘.tgz’ files containing binary package archives. Tilde-expansion will be done on file paths. If this is missing or a zero-length character vector, a listbox of available packages is presented where possible in an interactive R session.
`lib`	character vector giving the library directories where to install the packages. Recycled as needed. If missing, defaults to the first element of `.libPaths()`.
`repos`	character vector, the base URL(s) of the repositories to use, e.g., the URL of a CRAN mirror such as `"http://cran.us.r-project.org"`. For more details on supported URL schemes see `url`. Can be `NULL` to install from local files, directories or URLs: this will be inferred by extension from `pkgs` if of length one.
`contriburl`	URL(s) of the contrib sections of the repositories. Use this argument if your repository mirror is incomplete, e.g., because you burned only the ‘contrib’ section on a CD, or only have binary packages. Overrides argument `repos`. Can also be `NULL` to install from local files.
`method`	download method, see `download.file`.
`available`	an object as returned by `available.packages` listing packages available at the repositories, or `NULL` when the function makes an internal call to `available.packages`.
`destdir`	directory where downloaded packages are stored. If it is `NULL` (the default) a subdirectory `downloaded_packages` of the session temporary directory will be used (and the files will be deleted at the end of the session).
`dependencies`	logical indicating to also install uninstalled packages which these packages depend on/link to/import/suggest (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. If this is not the case it is ignored, with a warning. The default, `NA`, means `c("Depends", "Imports", "LinkingTo")`. `TRUE` means to use `c("Depends", "Imports", "LinkingTo", "Suggests")` for `pkgs` and `c("Depends", "Imports", "LinkingTo")` for added dependencies: this installs all the packages needed to run `pkgs`, their examples, tests and vignettes (if the package author specified them correctly). In all of these, `"LinkingTo"` is omitted for binary packages.
`type`	character, indicating the type of package to download and install. Possible values are (currently) `"source"`, `"mac.binary"`, `"mac.binary.mavericks"` and `"win.binary"`: the binary types can be listed and downloaded but not installed on other platforms. The default is the appropriate binary type on Windows and on the CRAN binary OS X distributions, otherwise `"source"`. For the platforms where binary packages are the default, an alternative is `"both"` which means ‘try binary if available and current, otherwise try source’. (This will only choose the binary package if its version number is no older than the source version. In interactive use it will ask before attempting to install source packages.)
`configure.args`	(Used only for source installs.) 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 re-used 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`	(Used only for source installs.) Analogous to `configure.args` for flag --configure-vars, which is used to set environment variables for the `configure` run.
`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 more than one source package. Values greater than one are supported if the `make` command specified by `Sys.getenv("MAKE", "make")` accepts argument `-k -j Ncpus`.
`verbose`	a logical indicating if some “progress report” should happen.
`libs_only`	a logical value: should the --libs-only option be used to install only additional sub-architectures? (See also `INSTALL_opts`.) This can also be used on Windows to install just the DLL(s) from a binary package, e.g. to add 64-bit DLLs to a 32-bit install.
`INSTALL_opts`	an optional character vector of additional option(s) to be passed to `R CMD INSTALL` for a source package install. E.g., `c("--html", "--no-multiarch")`. Can also be a named list of character vectors of to be used as additional options, with names the respective package names.
`quiet`	logical: if true, reduce the amount of output.
`keep_outputs`	a logical: if true, keep the outputs from installing source packages in the current working directory, with the names of the output files the package names with ‘.out’ appended. Alternatively, a character string giving the directory where to save the outputs. Ignored when installing from local files.
`...`	Arguments to be passed to `download.file` or to the functions for binary installs on OS X and Windows (which accept an argument `"lock"`: see the section on ‘Locking’).

Details

R packages are primarily distributed as source packages, but binary packages (a packaging up of the installed package) are also supported, and the type most commonly used on Windows and by the CRAN distributions for OS X. This function can install either type where supported, either by downloading a file from a repository or from a local file. The default type is given by getOption("pkgType"): this defaults to "source" apart from under Windows or a CRAN binary distribution for OS X.

This is the main function to install packages. 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 message if there is more than one.) If lib is omitted or is of length one and is not a (group) writable directory, in interactive use the code offers to create a personal library tree (the first element of Sys.getenv("R_LIBS_USER")) and install there.

For source packages from a repository 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).

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

Argument libs_only = TRUE is supported for source installs and for Windows binary installs.

For binary installs, the function also checks for the availability of a source package on the same repository, and reports if the source package has a later version, or is available but no binary version is. This check can be suppressed by

    options(install.packages.check.source = "no")

and should be if there is a partial repository containing only binary files.

Value

Invisible NULL.

Locking

There are various options for locking: these differ between source and binary installs.

By default for a source install, the library directory is ‘locked’ by creating a directory ‘00LOCK’ within it. This has two purposes: it prevents any other process installing into that library concurrently, and is used to store any previous version of the package to restore on error. A finer-grained locking is provided by the option --pkglock which creates a separate lock for each package: this allows enough freedom for parallel installation. Per-package locking is the default when installing a single package, and for multiple packages when Ncpus > 1L. Finally locking (and restoration on error) can be suppressed by --no-lock.

For an OS X or Windows binary install, no locking is done by default. Setting argument lock to TRUE (it defaults to the value of getOption("install.lock", FALSE)) will use per-directory locking as described for source installs: if the value is "pkglock" per-package locking will be used.

If package locking is used on Windows with libs_only = TRUE and the installation fails, the package will be restored to its previous state.

Note that it is possible for the package installation to fail so badly that the lock directory is not removed: this inhibits any further installs to the library directory (or for --pkglock, of the package) until the lock directory is removed manually.

Parallel installs

Parallel installs are attempted if pkgs has length greater than one and Ncpus > 1. It makes use of a parallel make, so the make specified (default make) when R was built must be capable of supporting make -j n: GNU make and dmake do, but FreeBSD and Solaris make do not: if necessary environment variable MAKE can be set for the current session to select a suitable make.

install.packages needs to be able to compute all the dependencies of pkgs from available, including if one element of pkgs depends indirectly on another. This means that if for example you are installing CRAN packages which depend on Bioconductor packages which in turn depend on CRAN packages, available needs to cover both CRAN and Bioconductor packages.

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.

Some binary Linux distributions of R can be installed on a machine without the tools needed to install packages: a possible remedy is to do a complete install of R which should bring in all those tools as dependencies.

Examples

## Not run: 
## A Linux example for Fedora's layout
install.packages(c("ncdf4", "RNetCDF"),
  configure.args = c(RNetCDF = "--with-netcdf-include=/usr/include/udunits2"))

## End(Not run)

[Package utils version 3.1.1 ]