Install dependencies in R

install.deps.R

# Load GO and DE data to R

## @knitr prep_data

# Install missing CRAN packages if needed

# git.packages <- c("docopt/docopt.R")
# github.packages <- c("argparser")
install.deps <- function(p, repo="cran"){
  call_install <- switch(repo,cran=c("install.packages(package, repos=\"http://cloud.r-project.org/\""),
                         bioc=c("biocLite(package, suppressUpdates=TRUE"),
                         git=c("install.github(package"))
  if (repo=="bioc") eval(parse(text = getURL("http://bioconductor.org/biocLite.R", ssl.verifypeer=FALSE)))
  for (package in p) {
    if (!package %in% installed.packages()) {
      cat(sprintf("Please wait, installing and loading missing package %s and its dependencies from %s.\n",
                  package, repo), file=stderr())
      suppressWarnings(eval(parse(text = sprintf("%s, quiet = TRUE)",call_install))))
      if (!package %in% installed.packages()) {
        ifelse(!interactive(),q("no", 2, TRUE),
               stop(sprintf("Unable to install missing package %s from %s.\n",
                            package, repo), call. = FALSE))
      }
    }
    require(package, character.only=TRUE, quietly=TRUE, warn.conflicts=TRUE)
  }
}


# Install and load cran packages
CRAN_packages <- c("RCurl", "pander", "grid", "RColorBrewer", "dplyr", "ggplot2", "knitr")
install.deps(CRAN_packages)

# Install and load bioconductor packages
bioc_packages <- c("qvalue","goseq", "GO.db")
install.deps(bioc_packages, repo="bioc")

# Reload dplyr (must be last package loaded)
detach("package:dplyr", unload=TRUE)
library(dplyr)