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basedir <- getwd()
run <- function(cmd) {
cat("RUNNING:", cmd, "\n")
ret <- system(cmd)
if (ret != 0) {
cat("ERROR running", cmd, "exiting\n")
quit(save="no", status=ret)
# Various Dependencies
cat("Installing various dependencies\n")
c("codetools", "foreach", "doMC", "getopt", "optparse",
"bigmemory", "biganalytics", "bigmemory.sri", "testthat")
, repos="")
c("plyr", "Rcpp", "RcppArmadillo", "inline", "devtools"),
, repos="")
# If devtools fails then you will need to manually download the libraries from git and install them
# Install BigAlgebra
cat("\nInstalling bigalgebra\n")
devtools::install_github("czarrar/bigalgebra") #
# Installing niftir and friends
cat("\nInstalling connectir and friends\n")
devtools::install_github("czarrar/bigextensions") #
devtools::install_github("czarrar/niftir") #
run("git clone") #
run("R CMD INSTALL connectir")
cat("\nCopying scripts for connectir\n")
bindir <- dirname(system("which R", intern=TRUE))
system(sprintf("cp connectir/inst/scripts/*.R %s/", bindir))
system(sprintf("rm -f %s/*_worker.R", bindir))
system(sprintf("chmod +x %s/*.R", bindir))
run("rm -rf connectir")
# TODO: add copying of scripts to some bin location
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