install {AnVIL}R Documentation

Discover and install binary packages for fast installation

Description

'install()': install R / Bioconductor packages, using fast pre-built 'binary' libraries if available.

'repositories()': repositories to search for binary (if available), Bioconductor, and CRAN packages.

'repository()': the location of the repository of binary packages for fast installation, if available.

'add_libpaths()': Add local library paths to '.libPaths()'.

Usage

install(
  pkgs = character(),
  ...,
  version = BiocManager::version(),
  binary_base_url = BINARY_BASE_URL
)

repositories(
  version = BiocManager::version(),
  binary_base_url = BINARY_BASE_URL
)

repository(version = BiocManager::version(), binary_base_url = BINARY_BASE_URL)

add_libpaths(paths)

Arguments

pkgs

'character()' packages to install from binary repository.

...

additional arguments, passed to 'BiocManager::install()'.

version

'character(1)' or 'package_version' Bioconductor version, e.g., "3.12".

binary_base_url

'character(1)' host and base path for binary package 'CRAN-style' repository; not usually required by the end-user.

paths

'character()': vector of directories to add to '.libPaths()'. Paths that do not exist will be created.

Details

'repositories()' prepends an additional repository URI to 'BiocManager::repositories()'. The URI is formed by concatenating 'binary_base_url', the environment variables ‘TERRA_R_PLATFORM' and the ’major' and 'minor' components of 'TERRA_R_PLATFORM_BINARY_VERSION' and 'BiocManager::version()'. The URI is only prepended if a CRAN-style repostiory exists at that location, with binary package tar.gz content described by 'src/contrib/PACKAGES.gz'.

The unexported URL to the base repository is available with 'AnVIL:::BINARY_BASE_URL'.

Value

'install()': return value of 'BiocManager::install()'.

'repositories()': character() of binary (if available), Bioconductor, and CRAN repositories.

'repository()': character(1) location of binary repository, if available, or character(0) if not.

'add_libpaths()': updated .libPaths(), invisibly.

Examples

## Not run: install(c('BiocParallel', 'BiocGenerics'))

repositories()

repository()

## Not run: add_libpaths("/tmp/host-site-library")


[Package AnVIL version 1.6.2 Index]