r-get

#! /usr/bin/env Rscript

#--------------------------------------------------------------
# An apt-get-like CLI interface for dealing with R packages
#--------------------------------------------------------------

home_dir <- Sys.getenv("HOME")
r_version <- paste(R.version$major, strsplit(R.version$minor, '.', fixed=TRUE)[[1]][[1]], sep=".")
mylib <- file.path(home_dir, "R/x86_64-pc-linux-gnu-library/", r_version)
max.cpus <- 1

help <- "
Usage: r-get <command> [args]

Commands:
  search - look for a package that matches a given string
  install - install one or more packages
  upgrade - upgrade all packages
  recompile - recompile all packages (useful for doing major version upgrades eg. 2.8.x -> 2.9.x)

Args:
  for search - a Perl-style regular expression
  install - one or more packages to install
"

argv <- commandArgs(TRUE)

if (length(argv) == 0 || argv[1] %in% c("help", "--help", "-help", "-h")) {
	cat(help)
	q(save="no")
}

# Try to detect the number of CPUs available and use them in parallel when
# making multiple packages
if (require(parallel, quietly=TRUE)) {
	detected_cpus <- detectCores()
	if (!is.na(detected_cpus)) {
		max.cpus <- detected_cpus
	}
}

# biocLite can be used to install all package types (bioconductor, CRAN, etc.),
# use it for everything.
source("http://bioconductor.org/biocLite.R")

# When interactive, use:
# chooseBioCmirror()
options(repos = biocinstallRepos())

if (argv[1] == "search") {
	all.packages <- available.packages()
	matches <- all.packages[grep(argv[-1], all.packages[,"Package"], perl=TRUE),]
	if (nrow(matches) > 0) {
		# Possible columns:
		#  Package Version  Priority Bundle Contains Depends Imports Suggests OS_type Repository
		#  Note: Package name is displayed automatically, don't need to print it.
		cols <- c("Version", "Depends")
		print(matches[,cols])
	} else {
		cat(paste("No matches found for query: ", argv[-1], "\n"))
	}
} else if (argv[1] == "install") {
	biocLite(argv[-1], lib.loc=mylib, lib=mylib, Ncpus=max.cpus)
} else if (argv[1] == "upgrade") {
	if (length(argv) <= 2) {
		cat("Upgrading all packages\n")
		# Leave out lib.loc to upgrade all library locations
		#update.packages(ask=FALSE, instlib=mylib, checkBuilt=TRUE)
		update.packages(lib.loc=mylib, ask=FALSE, instlib=mylib, checkBuilt=TRUE, Ncpus=max.cpus)
		#update.packages(ask=FALSE, instlib=mylib)
	}
} else if (argv[1] == "recompile") {
	# Sometimes useful after a major update (e.g. 2.15.x -> 2.16.x). Leave
	# argument blank to recompile everything. This isn't very well tested
	# since I've only used it once or twice.
	if (length(argv) >= 2) {
		pkgs <- argv[-1]
	} else {
		pkgs <- rownames(installed.packages())
	}
	biocLite(pkgs)
} else {
	cat(paste("Command not recognized:", argv[1]))
	cat(help)
	q(save="no")
}