bioc_all: Grab a copy of all bioconductor packages and install them by...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Grab a copy of all bioconductor packages and install them by type

Description

This uses jsonlite to get a copy of all bioconductor packages by name and then iterates through them with BiocManager to install all of them. It performs a sleep between each installation in an attempt to avoid being obnoxious. As a result, it will of a necessity take forever.

Usage

bioc_all(
  release = NULL,
  mirror = "bioconductor.statistik.tu-dortmund.de",
  base = "packages",
  type = "software",
  suppress_updates = TRUE,
  suppress_auto = TRUE,
  force = FALSE
)

Arguments

release	Bioconductor release to use, should probably be adjusted to automatically find it.
mirror	Bioconductor mirror to use.
base	Base directory on the mirror to download from.
type	Type in the tree to use (software or annotation)
suppress_updates	For BiocLite(), don't update?
suppress_auto	For BiocLite(), don't update?
force	Install if already installed?

Value

a number of packages installed

See Also

[BiocManager] [jsonlite]

Examples

## Not run: 
 go_get_some_coffee_this_will_take_a_while <- bioc_all()

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.