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Install a development package from the Bioconductor git repository

Source: R/install-bioc.R
install_bioc.Rd

This function requires git to be installed on your system in order to be used.

Usage

install_bioc(
  repo,
  mirror = getOption("BioC_git", download_url("git.bioconductor.org/packages")),
  git = c("auto", "git2r", "external"),
  dependencies = NA,
  upgrade = c("default", "ask", "always", "never"),
  force = FALSE,
  quiet = FALSE,
  build = TRUE,
  build_opts = c("--no-resave-data", "--no-manual", "--no-build-vignettes"),
  build_manual = FALSE,
  build_vignettes = FALSE,
  repos = getOption("repos"),
  type = getOption("pkgType"),
  ...
)

Arguments

repo

Repository address in the format [username:password@][release/]repo[#commit]. Valid values for the release are ‘devel’, ‘release’ (the default if none specified), or numeric release numbers (e.g. ‘3.3’).

mirror

The Bioconductor git mirror to use

git

Whether to use the git2r package, or an external git client via system. Default is git2r if it is installed, otherwise an external git installation.

dependencies

Which dependencies do you want to check? Can be a character vector (selecting from "Depends", "Imports", "LinkingTo", "Suggests", or "Enhances"), or a logical vector.

TRUE is shorthand for "Depends", "Imports", "LinkingTo" and "Suggests". NA is shorthand for "Depends", "Imports" and "LinkingTo" and is the default. FALSE is shorthand for no dependencies (i.e. just check this package, not its dependencies).

The value "soft" means the same as TRUE, "hard" means the same as NA.

You can also specify dependencies from one or more additional fields, common ones include:

  • Config/Needs/website - for dependencies used in building the pkgdown site.

  • Config/Needs/coverage for dependencies used in calculating test coverage.

upgrade

Should package dependencies be upgraded? One of "default", "ask", "always", or "never". "default" respects the value of the R_REMOTES_UPGRADE environment variable if set, and falls back to "ask" if unset. "ask" prompts the user for which out of date packages to upgrade. For non-interactive sessions "ask" is equivalent to "always". TRUE and FALSE are also accepted and correspond to "always" and "never" respectively.

force

Force installation, even if the remote state has not changed since the previous install.

quiet

If TRUE, suppress output.

build

If TRUE build the package before installing.

build_opts

Options to pass to R CMD build, only used when build is TRUE.

build_manual

If FALSE, don't build PDF manual ('--no-manual').

build_vignettes

If FALSE, don't build package vignettes ('--no-build-vignettes').

repos

A character vector giving repositories to use.

type

Type of package to update.

...

Other arguments passed on to utils::install.packages().

Details

It is vectorised so you can install multiple packages with a single command.

This is intended as an aid for Bioconductor developers. If you want to install the release version of a Bioconductor package one can use the BiocManager package.

See also

Other package installation: install_bitbucket(), install_cran(), install_dev(), install_github(), install_gitlab(), install_git(), install_local(), install_svn(), install_url(), install_version()

Examples

if (FALSE) {
install_bioc("SummarizedExperiment")
install_bioc("devel/SummarizedExperiment")
install_bioc("3.3/SummarizedExperiment")
install_bioc("SummarizedExperiment#abc123")
install_bioc("user:password@release/SummarizedExperiment")
install_bioc("user:password@devel/SummarizedExperiment")
install_bioc("user:password@SummarizedExperiment#abc123")
}