install.R

##############
# Check that the currently install version of R
# is at least the minimum required version
##############
R_min_version <- "3.1.0"
R_version <- paste0(R.Version()$major, ".", R.Version()$minor)

if (compareVersion(R_version, R_min_version) < 0) {
  stop(
    "You do not have the latest required.\n",
    "Launch will fail if you continue.\n",
    "Go to http://cran.r-project.org/ to update your version of R."
  )
}

######
# Install basic required packages if not available/installed
######
download_not_installed <- function(x) {
  availpacks <- .packages(all.available = TRUE)
  source("http://bioconductor.org/biocLite.R")
  missingPackages <- x[!(x %in% availpacks)]
  message("The following packages were missing. Installation attempted...")
  message(missingPackages)
  if (length(missingPackages) > 0) {
    for (i in missingPackages) {
      message("Installing", i, "package using biocLite...\n")
      biocLite(i)
    }
  }
}

vanilla_install_packages <- c(
  "limma",
  "markdown",
  "shiny",
  "shinyjs",
  "shinyBS",
  "scales",
  "markdown",
  "ggplot2",
  "png",
  "vsn",
  "RUnit",
  "reshape",
  "digest",
  "Rcpp",
  "VennDiagram",
  "convert"
)
download_not_installed(vanilla_install_packages)
###################################
# Should use latest version of shiny
###################################
shiny_okay <- FALSE
if ("shiny" %in% .packages(all.available = TRUE)) {
  shiny_min_version <- "0.11"
  shiny_compare <- compareVersion(as.character(packageVersion("shiny")), shiny_min_version)
  if (shiny_compare >= 0) {
    shiny_okay <- TRUE
  }
}

if (!shiny_okay) {
  install.packages("devtools")
  devtools::install_github("rstudio/shiny")
  devtools::install_github("trestletech/shinyTable")
}