local R package installation

3 files changed, 31 insertions, 22 deletions

diff --git a/ext/lazar/extconf.rb b/ext/lazar/extconf.rb
index a76f0f4..006e24c 100644
--- a/ext/lazar/extconf.rb
+++ b/ext/lazar/extconf.rb
@@ -1,8 +1,24 @@
 require 'fileutils'
 require 'rbconfig'
+require 'mkmf'
 
 main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..",".."))
 
+# check for required programs
+programs = ["R","Rscript","mongod","java","getconf"]
+programs.each do |program|
+  abort "Please install #{program} on your system." unless find_executable program
+end
+
+abort "Please install Rserve on your system. Execute 'install.packages('Rserve')' in a R console running as root ('sudo R')."  unless `R CMD Rserve --version`.match(/^Rserve/)
+
+# install R packages
+r_dir = File.join main_dir, "R"
+FileUtils.mkdir_p r_dir
+FileUtils.mkdir_p File.join(main_dir,"bin") # for Rserve binary
+rinstall = File.expand_path(File.join(File.dirname(__FILE__),"rinstall.R"))
+puts `Rscript --vanilla #{rinstall} #{r_dir}`
+
 # install OpenBabel
 
 openbabel_version = "2.3.2"
@@ -48,7 +64,4 @@ Dir.chdir build_dir do
   ENV["PKG_CONFIG_PATH"] = File.dirname(File.expand_path(Dir["#{install_dir}/**/openbabel*pc"].first))
 end
 
-ob_include= File.expand_path File.join(File.dirname(__FILE__),"../../openbabel/include/openbabel-2.0")
-ob_lib= File.expand_path File.join(File.dirname(__FILE__),"../../openbabel/lib")
-
 $makefile_created = true
diff --git a/ext/lazar/rinstall.R b/ext/lazar/rinstall.R
index 7c1510d..38e7377 100644
--- a/ext/lazar/rinstall.R
+++ b/ext/lazar/rinstall.R
@@ -1,7 +1,9 @@
-chooseCRANmirror(ind=19);
-install.packages("Rserve");
-install.packages("gridExtra");
-install.packages("ggplot2");
-install.packages("pls");
-install.packages("caret");
-install.packages("doMC");
+libdir = commandArgs(trailingOnly=TRUE)[1]
+# chooseCRANmirror(ind=19); does not have any impact on selected server
+#args=paste0("--prefix=",libdir,"/..")
+#install.packages("Rserve",lib=libdir,configure.args=args)
+install.packages("gridExtra",lib=libdir);
+install.packages("ggplot2",lib=libdir);
+install.packages("pls",lib=libdir);
+install.packages("caret",lib=libdir);
+install.packages("doMC",lib=libdir);
diff --git a/lib/lazar.rb b/lib/lazar.rb
index b4293e9..22dfd2b 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -40,17 +40,18 @@ when "development"
 end
 
 # R setup
+rlib = File.expand_path(File.join(File.dirname(__FILE__),"..","R"))
 # should work on POSIX including os x
 # http://stackoverflow.com/questions/19619582/number-of-processors-cores-in-command-line
 NR_CORES = `getconf _NPROCESSORS_ONLN`.to_i
 R = Rserve::Connection.new
 R.eval "
 suppressPackageStartupMessages({
-  library(ggplot2)
-  library(grid)
-  library(gridExtra)
-  library(caret)
-  library(doMC)
+  library(ggplot2,lib=\"#{rlib}\")
+  library(grid,lib=\"#{rlib}\")
+  library(gridExtra,lib=\"#{rlib}\")
+  library(caret,lib=\"#{rlib}\")
+  library(doMC,lib=\"#{rlib}\")
   registerDoMC(#{NR_CORES})
 })
 "
@@ -58,13 +59,6 @@ suppressPackageStartupMessages({
 # Require sub-Repositories
 require_relative '../openbabel/lib/openbabel'
 
-# Fminer environment variables
-ENV['FMINER_SMARTS'] = 'true'
-ENV['FMINER_NO_AROMATIC'] = 'true'
-ENV['FMINER_PVALUES'] = 'true'
-ENV['FMINER_SILENT'] = 'true'
-ENV['FMINER_NR_HITS'] = 'true'
-
 # OpenTox classes and includes
 CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules