From 90fbe8b3ef3fa05aa308e6650e11d690bb89b200 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 24 Mar 2016 13:43:27 +0100
Subject: local R package installation

---
 ext/lazar/extconf.rb | 19 ++++++++++++++++---
 ext/lazar/rinstall.R | 16 +++++++++-------
 2 files changed, 25 insertions(+), 10 deletions(-)

(limited to 'ext')

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);
-- 
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