R: Download Packages from CRAN-like repositories

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compare the version numbers of installed packages with the newest available version on the repositories and update outdated packages on the fly.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")),
                       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"))

### Arguments

`lib.loc` | character vector describing the location of R library trees to search through (and update packages therein).
`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`.
`installWithVers` | If `TRUE`, will invoke the install of the package such that it can be referenced by package version.
`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", "Suggests")`. Note that only if the dependent package is installed is checked, not if it meets the version requirements. 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")` if `lib` is unambiguous, and `FALSE` otherwise.
`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 `--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 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`.
`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 are `"source"` (the default except under the CRAN Mac OS X build), `"mac.binary"` and `"win.binary"` (which can be downloaded but not installed).
`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.
`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.

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

`old.packages` compares the information from `available.packages` with that from `instPkgs` (`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 2.0.x when running R 2.1.1).

`new.packages` does the same comparison but reports uninstalled packages/bundles that are available at the repositories. (It checks the front-end package gnomeGUI separately.) 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`. NB: versioned installs are not installs of a named package.

`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"`, `"Depends"`, `"Imports"`, `"Suggests"` `"Contains"` 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 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 2.8.1 Index]