R/BiocManager-pkg.R

#' @importFrom utils packageVersion contrib.url head
#'     installed.packages sessionInfo tail
NULL

#' Install or update Bioconductor, CRAN, or GitHub packages
#'
#' This package provides tools for managing _Bioconductor_ and other
#' packages in a manner consistent with _Bioconductor_'s package
#' versioning and release system.
#'
#' @details
#'
#' Main functions are as follows; additional help is available for
#' each function, e.g., `?BiocManager::version`.
#'
#' - `BiocManager::install()`: Install or update packages from
#'   _Bioconductor_, CRAN, and GitHub.
#'
#' - `BiocManager::version()`: Report the version of _Bioconductor_ in
#'     use.
#'
#' - `BiocManager::available()`: Return a `character()` vector of
#'   package names available (at `BiocManager::repositories()`) for
#'   installation.
#'
#' - `BiocManager::valid()`: Determine whether installed packages are
#'     from the same version of _Bioconductor_.
#'
#' - `BiocManager::repositories()`: _Bioconductor_ and other
#'    repository URLs to discover packages for installation.
#'
#' The version of _Bioconductor_ in use is determined by the installed
#' version of a second package, BiocVersion. BiocVersion is installed
#' automatically during first use of `BiocManager::install()`. If
#' BiocVersion has not yet been installed, the version is determined
#' by code in base R.
#'
#' Options influencing package behavior (see `?options`, `?getOption`)
#' include:
#'
#' - `"repos"`, `"BiocManager.check_repositories"`,
#'   `"BiocManager.snapshot"`: URLs of additional repositories for use
#'   by `BiocManger::install()`. See `?repositories`.
#'
#' - `"pkgType"`: The default type of packages to be downloaded and
#'   installed; see `?install.packages`.
#'
#' - `"timeout"`: The maximum time allowed for download of a single
#'   package, in seconds. _BiocManager_ increases this to 300 seconds
#'   to accommodate download of large BSgenome and other packages.
#'
#' System environment variables influencing package behavior include:
#'
#' - \env{BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS} advanced
#'   configuration to avoid _Bioconductor_ version checks. See
#'   `?install`.
#'
#' @md
#' @name BiocManager-pkg
#' @aliases BiocManager
#' @docType package
#'
#' @examples
#' R.version.string
#' packageVersion("BiocManager")
#' if (requireNamespace("BiocVersion", quietly = TRUE))
#'     packageVersion("BiocVersion")
#' BiocManager::version()
"_PACKAGE"

Try the BiocManager package in your browser

Any scripts or data that you put into this service are public.

BiocManager documentation built on May 20, 2022, 1:14 a.m.