awsSetupScript.r

#' Simplified loading and installing of packages
#'
#' This is a wrapper to \code{\link{require}} and \code{\link{install.packages}}.
#' Specifically, this will first try to load the package(s) and if not found
#' it will install then load the packages. Additionally, if the 
#' \code{update=TRUE} parameter is specified it will check the currently 
#' installed package version with what is available on CRAN (or mirror) and 
#' install the newer version.
#' 
#' @param pkgs a character vector with the names of the packages to load.
#' @param install if TRUE (default), any packages not already installed will be.
#' @param update if TRUE, this function will install a newer version of the
#'        package if available.
#' @param quiet if TRUE (default), package startup messages will be suppressed.
#' @param verbose if TRUE (default), diagnostic messages will be printed.
#' @param ... other parameters passed to \code{\link{require}}, 
#'            \code{\link{install.packages}}, and 
#'            \code{\link{available.packages}}.
#' @return a data frame with four columns and rownames corresponding to the
#'         packages to be loaded. The four columns are: loaded (logical 
#'         indicating whether the package was successfully loaded), installed 
#'         (logical indicating that the package was installed or updated), 
#'         loaded.version (the version string of the installed package), and 
#'         available.version (the version string of the package currently 
#'         available on CRAN). Note that this only reflects packages listed in 
#'         the \code{pkgs} parameter. Other packages may be loaded and/or 
#'         installed as necessary by \code{install.packages} and \code{require}.
#'         If \code{verbose=FALSE} the data frame will be returned using 
#'         \code{\link{invisible}}.
#' @export
#' @example
#' \dontrun{
#' package(c('devtools','lattice','ggplot2','psych'))
#' }
package <- function(pkgs, install=TRUE, update=FALSE, quiet=TRUE, verbose=TRUE, ...) {
  myrequire <- function(package, ...) {
    result <- FALSE
    if(quiet) { 
      suppressMessages(suppressWarnings(result <- require(package, ...)))
    } else {
      result <- suppressWarnings(require(package, ...))
    }
    return(result)
  }
  mymessage <- function(msg) {
    if(verbose) {
      message(msg)
    }
  }
  
  installedpkgs <- installed.packages()
  availpkgs <- available.packages()[,c('Package','Version')]
  if(nrow(availpkgs) == 0) {
    warning(paste0('There appear to be no packages available from the ',
                   'repositories. Perhaps you are not connected to the ',
                   'Internet?'))
  }
  # It appears that hyphens (-) will be replaced with dots (.) in version
  # numbers by the packageVersion function
  availpkgs[,'Version'] <- gsub('-', '.', availpkgs[,'Version'])
  results <- data.frame(loaded=rep(FALSE, length(pkgs)),
                        installed=rep(FALSE, length(pkgs)),
                        loaded.version=rep(as.character(NA), length(pkgs)),
                        available.version=rep(as.character(NA), length(pkgs)),
                        stringsAsFactors=FALSE)
  row.names(results) <- pkgs
  for(i in pkgs) {
    loadedPkgs <- search()
    needInstall <- FALSE
    if(i %in% row.names(installedpkgs)) {
      v <- as.character(packageVersion(i))
      if(i %in% row.names(availpkgs)) {
        if(v != availpkgs[i,'Version']) {
          if(!update) {
            mymessage(paste0('A newer version of ', i, 
                             ' is available ', '(current=', v, 
                             '; available=',
                             availpkgs[i,'Version'], ')'))
          }
          needInstall <- update
        }
        results[i,]$available.version <- availpkgs[i,'Version']
      } else {
        mymessage(paste0(i, ' is not available on the repositories.'))
      }
    } else {
      if(i %in% row.names(availpkgs)) {
        needInstall <- TRUE & install
        results[i,]$available.version <- availpkgs[i,'Version']
      } else {
        warning(paste0(i, ' is not available on the repositories and ',
                       'is not installed locally'))
      }
    }
    if(needInstall | !myrequire(i, character.only=TRUE)) {
      install.packages(pkgs=i, quiet=quiet)
      if(!myrequire(i, character.only=TRUE, ...)) {
        warning(paste0('Error loading package: ', i))
      } else {
        results[i,]$installed <- TRUE
        results[i,]$loaded <- TRUE
        results[i,]$loaded.version <- as.character(packageVersion(i))
      }
    } else {
      results[i,]$loaded <- TRUE
      results[i,]$loaded.version <- as.character(packageVersion(i))
    }
    loadedPkgs2 <- search()
    for(j in loadedPkgs2[!loadedPkgs2 %in% loadedPkgs]) {
      try(detach(j, character.only=TRUE), silent=TRUE)
    }
  }
  if(verbose) {
    return(results)
  } else {
    invisible(results)
  }
}


#RUN THESE ON LINUX
#
#
#sudo apt-get install libcurl4-openssl-dev
#sudo apt-get install openjdk-7-*
#sudo R CMD javareconf
#sudo apt-get install r-cran-rjava
#



#install and load required packages
package(c("Rserve","devtools","gridExtra","rpart","rJava","RWeka","ISLR","pracma","dplyr","jsonlite","reshape2","e1071","kknn","cluster","caret","nnet","neuralnet"))
library(devtools)
install_github("mongosoup/rmongodb")