extconf.rb in lazar-0.0.9

- old
+ new
@@ -1,88 +1,27 @@
 require 'fileutils'
 require 'rbconfig'
+require 'mkmf'
 
 main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..",".."))
 
-# install OpenBabel
-
-
-openbabel_version = "2.3.2"
-
-openbabel_dir = File.join main_dir, "openbabel"
-src_dir = openbabel_dir #File.join openbabel_dir, "openbabel-#{openbabel_version}"
-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 = `grep processor /proc/cpuinfo | wc -l` # speed up compilation, Linux only
-rescue
-  nr_processors = 1
+# 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
 
-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
+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/)
 
-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
+# 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}`
 
-# 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
 
-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")
-
-# compile ruby bindings
-=begin
-puts "Compiling and installing OpenBabel Ruby bindings."
-Dir.chdir ruby_src_dir do
-  # fix rpath
-  system "sed -i 's|with_ldflags.*$|with_ldflags(\"#\$LDFLAGS -dynamic -Wl,-rpath,#{install_lib_dir}\") do|' #{File.join(ruby_src_dir,'extconf.rb')}"
-  system "#{RbConfig.ruby} extconf.rb --with-openbabel-include=#{ob_include} --with-openbabel-lib=#{ob_lib}"
-  system "make -j#{nr_processors}"
-end
-=end
-
-# install fminer
-fminer_dir = File.join main_dir, "libfminer"
-system "git clone git://github.com/amaunz/fminer2.git #{fminer_dir}"
-
-["libbbrc","liblast"].each do |lib|
-  FileUtils.cd File.join(fminer_dir,lib)
-  system "sed -i 's,^INCLUDE_OB.*,INCLUDE_OB\ =\ #{ob_include},g' Makefile" 
-  system "sed -i 's,^LDFLAGS_OB.*,LDFLAGS_OB\ =\ #{ob_lib},g' Makefile"
-  system "sed -i 's,^INCLUDE_RB.*,INCLUDE_RB\ =\ #{RbConfig::CONFIG['rubyhdrdir']},g' Makefile" 
-  # TODO fix in fminer Makefile
-  system "sed -i 's,-g, -g -I #{RbConfig::CONFIG['rubyhdrdir']} -I #{RbConfig::CONFIG['rubyarchhdrdir']} -I,' Makefile" # fix include path (CH)
-  system "sed -i '74s/$(CC)/$(CC) -Wl,-rpath,#{ob_lib.gsub('/','\/')} -L/' Makefile" # fix library path (CH)
-  system "make ruby"
-end
-
-# install last-utils
-FileUtils.cd main_dir
-system "git clone git://github.com/amaunz/last-utils.git"
-FileUtils.cd File.join(main_dir,"last-utils")
-`sed -i '8s/"openbabel", //' lu.rb`
-
-# install R packagemain_dir
 $makefile_created = true