Giotto Suite GitHub Installation

Installation convenience function. Helps with Giotto Suite installation from the GitHub website by ensuring modules are installed in the correct order. Also automatically switches to the R4.4.0 version when user R version is lower than 4.4.1.

This utility will do a full reinstall of the specified Giotto Suite modules but non-Suite dependencies will never prompt to be updated.

Usage

suite_install(
  modules = suite_packages(),
  suite_deps = TRUE,
  ref = "main",
  dry_run = FALSE,
  ...
)

Arguments

modules

character. Which modules to install. Defaults to the core packages needed for Giotto to run.

suite_deps

logical. Whether to install any potential Giotto Suite dependency modules

ref

character. Currently one of "main", "R4.4.0", or "dev". These determine which branches to install. See details.

dry_run

logical. When TRUE, only print the install commands instead of actually running them.

...

additional params to pass to remotes::install_github()

ref "main"

Installs the main Giotto version. This version is expected to chase the highest R version.

ref "R4.4.0", r440, or 440

Mirrors the main branch, but locks the R version at 4.4.0 (lowest version supported by all dependencies)

ref "R4.1.0", r410, or 410

Mirrors the main branch, but locks the R version at 4.1.0. This version requires installation of {Matrix} 1.6-5

ref "dev"

This version is ahead of the main version and also chases the latest R version.

Examples

if (FALSE) {
    # install core packages
    suite_install()
    suite_install("GiottoClass", ref = "dev")

    # install ONLY Giotto, ignoring module dependencies
    # (i.e. GiottoVisuals, GiottoClass, etc)
    suite_install("Giotto", suite_deps = FALSE)
}