install: Discover binary packages for fast installation

In Bioconductor/AnVIL: Bioconductor on the AnVIL compute environment

Discover binary packages for fast installation

Description

install() is deprecated in favor of BiocManager::install().

repository() is deprecated in favor of BiocManager::containerRepository().

repositories() is deprecated in favor of BiocManager::repositories().

⁠repository_stats():⁠ summarize binary packages compatible with the Bioconductor or Terra container in use.

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

Usage

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

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

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

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

## S3 method for class 'repository_stats'
print(x, ...)

add_libpaths(paths)

Arguments

pkgs	character() packages to install from binary repository.
...	additional arguments. install() passes additional arguments to BiocManager::install(). print.repository_stats() ignores the additional arguments.
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.
x	the object returned by repository_stats().
paths	character(): vector of directories to add to .libPaths(). Paths that do not exist will be created.

Value

repository_stats() returns a list of class repository_stats with the following fields:

• container: character(1) container label, e.g., bioconductor_docker, or NA if not evaluated on a supported container

• bioconductor_version: package_version the Bioconductor version provided by the user.

• repository_exists: logical(1) TRUE if a binary repository exists for the container and Bioconductor_Version version.

• bioconductor_binary_repository: character(1) repository location, if available, or NA if the repository does not exist.

• n_software_packages: integer(1) number of software packages in the Bioconductor source repository.

• n_binary_packages: integer(1) number of binary packages available. When a binary repository exists, this number is likely to be larger than the number of source software packages, because it includes the binary version of the source software packages, as well as the (possibly CRAN) dependencies of the binary packages

• n_binary_software_packages: integer(1) number of binary packages derived from Bioconductor source packages. This number is less than or equal to n_software_packages.

• missing_binaries: integer(1) the number of Bioconductor source software packages that are not present in the binary repository.

• out_of_date_binaries: integer(1) the number of Bioconductor source software packages that are newer than their binary counterpart. A newer source software package might occur when the main Bioconductor build system has updated a package after the most recent run of the binary build system.

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

Functions

• print(repository_stats): Print a summary of package availability in binary repositories.

Examples

stats <- repository_stats() # obtain statistics
stats                       # display a summary
stats$container             # access an element for further computation

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

Bioconductor/AnVIL documentation built on Oct. 28, 2023, 10:17 a.m.