cytoverse_update: Update cytoverse packages

In RGLab/cytoverse: Easily Install and Load the 'cytoverse'

Description

This will check to see if all cytoverse packages (and optionally, their dependencies) are up-to-date and installl those that are behind. The repo argument will determine whether to update from Bioconductor or GitHub and the pkgs argument allows for specification of a subset of packages to update.

Usage

cytoverse_update(
  repo = "bioconductor",
  pkgs = NULL,
  branch = NULL,
  check_versions = TRUE,
  upgrades_approved = FALSE,
  ...
)

Arguments

repo	either "bioconductor" or "github", specifying repository source
pkgs	A character vector containing a specific subset of cytoverse packages to check for updates. If NULL, all cytoverse packages will be checked. For the full list of packages, see cytoverse_packages.
branch	optionally allows specification of a branch within the repository. For Bioconductor, this corresponds to the version (e.g. "3.11" or "devel") and will default to the value of BiocManager::version(). For GitHub, this refers to branch from the GitHub repositories and will default to "master".
check_versions	a logical indicating whether the package versions should be checked to determine which packages to update. This defaults to TRUE, but if switched to FALSE, installation will default to checking commit SHA. This can be used to force updates for commits between version increments.
upgrades_approved	a logical indicating whether the user should be asked to approve/disapprove the proposed package updates. Defaults to FALSE, but If set to TRUE, the interactive prompt will be skipped and the updates will proceed automatically.
...	Other arguments passed to either BiocManager::install or remotes::install_github

Details

This utilizes either BiocManager::install for Bioconductor or remotes::install_github to check for package updates to install. As such, additional arguments can be passed to either of those methods. Please see the examples for the most typical use cases. If repo="bioconductor" is used and BiocManager is unavailable, it will be installed.

Examples

## Not run: 
# Default behavior. Update all cytoverse packages from
# appropriate Bioconductor release. Asks for approval of proposed updates.
cytoverse_update()

# Same as above, but do not ask for approval before proceeding with installation
cytoverse_update(upgrades_approved = TRUE)

# Still using appropriate Bioconductor release, but limiting to just checking
# a few packages for updates. check_versions = FALSE makes the method attempt to
# update all packages, relying on commit SHA to determine if packages are up-to-date
cytoverse_update(pkgs = c("flowWorkspace", "CytoML"), check_versions = FALSE)

# Specify that you would like to use the current development branches from Bioconductor
cytoverse_update(version = "devel")

# Override default repository (Bioconductor) to instead install from GitHub
cytoverse_update(repo = "github")

# An example showing extra arguments being passed down to install_github.
# Only update cytoqc and all of its dependencies (including from "Suggests" and "Enhances" sections)
cytoverse_update(repo = "github", pkgs = "cytoqc", dependencies = TRUE)


## End(Not run)

RGLab/cytoverse documentation built on July 17, 2020, 11:38 p.m.