pgr0ss

desc "install R packages"
  task :install_R_packages do
    R_packages = File.read("#{release_path}/R_packages.txt").lines.map { |line| line.strip }

    R_package_cmd = R_packages.map do |package|
      R_package_cmd << 'if(!require(\"'+package+'\")){ install.packages(\"'+package+'\",lib=c(\"'+shared_path+'/R\"), repos=\"http://cran.cnr.berkeley.edu/\"); };'
    end.join(' ')

    sudo "sh -c 'if [ ! -d #{shared_path}/R ]; then mkdir #{shared_path}/R; fi'"
    sudo "sh -c 'export R_LIBS_USER=#{shared_path}/R && R --vanilla -e \"#{R_package_cmd}\"'"