[R] Load packages

cran_pkg_load.R

#!/usr/bin/env Rscript

load_pkgs <- function(pkgs, repos = 'http://cran.rstudio.com/') {
  update.packages(checkBuilt = TRUE, ask = FALSE, repos = repos)
  sapply(pkgs,
         function(p) {
           if (! p %in% installed.packages()[,1]) install.packages(p, dependencies = TRUE, repos = repos)
           require(p, character.only = TRUE)
         })
}

# example
load_pkgs(pkgs = c('dplyr',
                   'data.table',
                   'RSQLite',
                   'foreach',
                   'doSNOW',
                   'ggplot2'))

install_bioconductor.R

source('http://bioconductor.org/biocLite.R')
biocLite()

install_rmpi.R

# export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/

install.packages('Rmpi',
                 configure.args = c('--with-Rmpi-include=/usr/include/openmpi-x86_64/',  # where mpi.h is located
                                    '--with-Rmpi-libpath=/usr/lib64/openmpi/lib/',       # where libmpi.so is located
                                    '--with-Rmpi-type=OPENMPI'))

install_rstan.R

Sys.setenv(MAKEFLAGS = '-j4')
source('http://mc-stan.org/rstan/install.R', echo = TRUE, max.deparse.length = 2000)
install_rstan()