Install r packages from CRAN, bioconductor and github and load them all with a single function.

install_from_dif_sources.R

install_cran <- function(cran_packages) {
	pkgs.To.Install = which(! cran_packages %in% installed.packages())
	if (length(pkgs.To.Install) != 0) {
		install.packages(cran_packages[pkgs.To.Install])
	}
	return(NULL)
}

install_bioconductor <- function(bioconductor_packages) {
	if (!require("BiocManager", quietly = TRUE)){
		install.packages("BiocManager")}
	pkgs.To.Install = which(! bioconductor_packages %in% installed.packages())
	
	if (length(pkgs.To.Install) != 0) {
		BiocManager::install(bioconductor_packages[pkgs.To.Install])	
	}
	return(NULL)
}

install_from_github <- function(github_packages) {
	if (! "devtools" %in% installed.packages()) {
		install.packages("devtools")
	}
	repos.github = github_packages
	# In the line below, we remove the folder name
	pkgs.github = gsub(".+/", "", repos.github)
	pkgs.To.Install = which(! pkgs.github %in% installed.packages())
	
	if (length(pkgs.To.Install) != 0) {
		# To install the package, we need the folder + package name
		devtools::install_github(repos.github[pkgs.To.Install])	
	}
	return(pkgs.github)
}
install_from_dif_sources <- function(
	cran_packages = c(),	
	bioconductor_packages = c(),
	github_packages = c()) {
	all_packages = c(cran_packages, bioconductor_packages)
	
	#### Install from CRAN ####
	if (length(cran_packages) != 0) install_cran(cran_packages)
	#### Install from Bioconductor ####
	if (length(bioconductor_packages) != 0) install_bioconductor(
		bioconductor_packages
		)
	#### Install from github ####
	if (length(github_packages) != 0) {
		all_packages = c(all_packages, 
				 install_from_github(github_packages)
		)
	}
	for (curPkg in all_packages) library(curPkg, character.only = T) 
	return("All done!")
}