From 76d30230f589026d7019ddbfa8ae0a511e171e27 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 31 Mar 2016 10:04:42 +0200
Subject: lazar gem, version bumped to 0.9

---
 ext/lazar/extconf.rb | 46 +++-------------------------------------------
 ext/lazar/rinstall.R | 13 ++++++-------
 2 files changed, 9 insertions(+), 50 deletions(-)

(limited to 'ext')

diff --git a/ext/lazar/extconf.rb b/ext/lazar/extconf.rb
index 006e24c..a577baa 100644
--- a/ext/lazar/extconf.rb
+++ b/ext/lazar/extconf.rb
@@ -19,49 +19,9 @@ 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"
-
-openbabel_dir = File.join main_dir, "openbabel"
-src_dir = openbabel_dir 
-build_dir = File.join src_dir, "build"
-install_dir = openbabel_dir 
-install_lib_dir = File.join install_dir, "lib"
-lib_dir = File.join openbabel_dir, "lib", "openbabel"
-ruby_src_dir = File.join src_dir, "scripts", "ruby"
-
-begin
-  nr_processors = `getconf _NPROCESSORS_ONLN`.to_i # should be POSIX compatible
-rescue
-  nr_processors = 1
-end
-
-FileUtils.mkdir_p openbabel_dir
-Dir.chdir main_dir do
-  FileUtils.rm_rf src_dir
-  puts "Downloading OpenBabel sources"
-  system "git clone https://github.com/openbabel/openbabel.git"
-end
-
-FileUtils.mkdir_p build_dir
-FileUtils.mkdir_p install_dir
-Dir.chdir build_dir do
-  puts "Configuring OpenBabel"
-  cmake = "cmake #{src_dir} -DCMAKE_INSTALL_PREFIX=#{install_dir} -DBUILD_GUI=OFF -DENABLE_TESTS=OFF -DRUN_SWIG=ON -DRUBY_BINDINGS=ON"
-  # set rpath for local installations
-  # http://www.cmake.org/Wiki/CMake_RPATH_handling
-  # http://vtk.1045678.n5.nabble.com/How-to-force-cmake-not-to-remove-install-rpath-td5721193.html
-  cmake += " -DCMAKE_INSTALL_RPATH:STRING=\"#{install_lib_dir}\"" 
-  system cmake
-end
-
-# local installation in gem directory
-Dir.chdir build_dir do
-  puts "Compiling OpenBabel sources."
-  system "make -j#{nr_processors}"
-  system "make install"
-  ENV["PKG_CONFIG_PATH"] = File.dirname(File.expand_path(Dir["#{install_dir}/**/openbabel*pc"].first))
+# create a fake Makefile
+File.open(File.join(File.dirname(__FILE__),"Makefile"),"w+") do |makefile|
+  makefile.puts "all:\n\ttrue\n\ninstall:\n\ttrue\n"
 end
 
 $makefile_created = true
diff --git a/ext/lazar/rinstall.R b/ext/lazar/rinstall.R
index 38e7377..4e4fac7 100644
--- a/ext/lazar/rinstall.R
+++ b/ext/lazar/rinstall.R
@@ -1,9 +1,8 @@
 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);
+repo = "https://stat.ethz.ch/CRAN/"
+install.packages("gridExtra",lib=libdir,repos=repo);
+install.packages("ggplot2",lib=libdir,repos=repo);
+install.packages("pls",lib=libdir,repos=repo);
+install.packages("caret",lib=libdir,repos=repo);
+install.packages("doMC",lib=libdir,repos=repo);
-- 
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