install.pkgs: Enhanced Package Installation
In renozao/repotools: Tools for R Package Repositories

Description Usage Arguments Details Repositories

These functions are enhanced versions of the base functions install.packages, available.packages and link{download.packages} (see Details).

install.pkgs(pkgs, lib = NULL, repos = getOption("repos"),
  type = getOption("pkgType"), dependencies = NA, available = NULL, ...,
  reload = FALSE, upgrade_dependencies = FALSE, quick = FALSE,
  dry.run = NULL, devel = FALSE, verbose = TRUE)

`pkgs`	character vector of the names of packages whose current versions should be downloaded from the repositories or of path to source/binary package files (or a mixed of both).
`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`	URL or specification of CRAN-like package repository (see section Repositories). Use `repos = '+http://myrepo.org'` to append repositories to the default ones.
`type`	character, indicating the type of package to download and install. Will be `"source"` except on Windows and some macOS builds: see the section on ‘Binary packages’ for those.
`dependencies`	logical indicating whether 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.
`available`	a matrix as returned by `available.packages` listing packages available at the repositories, or `NULL` when the function makes an internal call to `available.packages`. Incompatible with `type = "both"`.
`...`	extra parameters eventually passed to the corresponding base function.
`reload`	if `TRUE` (the default), will automatically reload the package after installing.
`upgrade_dependencies`	If `TRUE`, the default, will also update any out of date dependencies.
`quick`	if `TRUE` skips docs, multiple-architectures, demos, and vignettes, to make installation as fast as possible.
`dry.run`	logical that indicates if one should only return the computed set of packages and dependencies to install. If `NULL`, then it is internally set to `TRUE` only when there is a mismatch between the requested and the OS binary package types (e.g., if `type = 'win.both'` on a Unix/Mac host).
`devel`	indicates if development packages hosted on GRAN (GitHub) should be preferred to versions available in regular repositories. The following values are allowed: `FALSE`: package versions on regular repositories have priority over all other versions. `TRUE`: 'release' GRAN versions (i.e. from master branches) are preferred to versions on regular repositories (if their version is number is larger) and 'devel' development versions (i.e. on branches that start with 'devel'). `2`: 'devel' GRAN versions are preferred over all other versions. In any case, packages not found in regular repositories are looked up on GRAN release, then GRAN devel if still not found.
`verbose`	verbosity level (logical or numeric)

The main differences with the base functions are that:

Bioconductor (soft, data/annotation, etc..) and Omegahat dependencies are automatically resolved, without the need to enable these repositories;
if necessary, they use an enhanced curl binary that internally uses the RCurl package, which is configured to support authentication for password protected repositories. Credentials can either passed embbedded within the URL or transparently taken from the user's .netrc file;
it supports the mixed-type installation, of binary and source packages;
it can install packages and recursive dependencies hosted on GitHub, if these have been hooked to the GRAN repository.

install.pkgs installs packages, which can be local, remote or in a CRAN-like repository, possibly password protected. Packages and their dependencies are automatically search in Bioconductor, Omegahat and GRAN repositories if needed.

Respositories can be specified as a character vector that is processed in the following way:

repos = NULL, then the default set of repositories defined in option 'repos' are used (see getOption('repos'));
repos = c('+http://one.repo.org', 'http://two.repo.org') appends one or more repositories to the default set of repositories.
if an element of repos is '@CRAN@', then the user is asked to choose a CRAN mirror, except if in non-interactive mode, where RStudio mirror is used (http://cran.rstudio.com);
Full URL, that can be remote (start with 'http://') or local (start with file://), and may include authentication credentials in the form 'http://username:password@cran.domain.org', for password protected repositories (Basic, Digest, etc..);
Repo URL shortcut key (+ path), defined as a string prefixed with '@', e.g., '@myRepo/path/to/repo', that matches a repository entry in file '.netrc' in the user's home directory – as returned by Sys.getenv('HOME'). It is internally substituted into a full repository base URL using by repos_url (see details in read_netrc and repos_url for details on how repository entries are defined and substituted respectively.