R4rb 1.0.0

data/ext/R4rb/extconf.rb

@@ -0,0 +1,133 @@
+# encoding: utf-8
+require "mkmf"
+require 'fileutils' #if RUBY_VERSION < "1.9"
+
+# TODO: specify a file R4rb.conf to provide multiple R systems location
+# in lib/R4rb.rb read this file to offer the several choices
+
+def find_installed_R
+
+  if RUBY_PLATFORM=~/mingw/ or RUBY_PLATFORM=~/msys/
+    $prefix=`R RHOME`.gsub("\\","/")
+    $prefix_include=$prefix+"/include"
+    $prefix_lib=nil
+    (RUBY_PLATFORM=~/64/ ? ["","x64"] : ["","i386"]).each do |arch|
+        $prefix_lib=File.join($prefix,"bin",arch) if File.exists? File.join($prefix,"bin",arch,"R.dll")
+        #$versions=[arch]
+        break if $prefix_lib
+    end
+  elsif RUBY_PLATFORM=~/darwin/
+    versions="/Library/Frameworks/R.framework/Versions"
+    if File.directory? versions  
+        $prefix=Dir[versions+"/*/Resources"].select{|e| e.split("/")[-2]!="Current"}
+        $prefix_include=$prefix.map{|e| e+"/include"}
+        $prefix_lib=$prefix.map{|e| e+"/lib"}
+        $versions=$prefix.map{|e| e.split("/")[-2]}
+    else
+        $prefix=`R RHOME`.strip
+        $prefix_include=$prefix+"/include"
+        $prefix_lib=$prefix+"/lib"
+    end
+    
+  else
+    stddirs=["/usr/local/lib/R","/usr/lib/R","/usr/share/R","/usr/include/R","/usr/lib64/R"]
+    stddirs.unshift `R RHOME`.strip.split("\n").select{|l| l=~/^\//}[0] unless `R RHOME`.empty?
+    usrdirs = []
+    ARGV.each do |arg|
+        if arg =~ /--with-R/
+            option, value = arg.split('=')
+            usrdirs = [ value ] + usrdirs
+        end
+    end
+    dirs = usrdirs + stddirs
+    dirs.uniq! # remove duplicates 
+
+    $prefix,$prefix_include,$prefix_lib=nil,nil,nil
+
+    dirs.each do |dir|
+        p dir
+        if !$prefix and FileTest.exists?(dir)
+            $prefix = dir[0..-3]
+        end
+    
+        if !$prefix_include and FileTest.exists?(dir+"/include/R.h")
+            $prefix_include=dir+"/include"
+        end
+
+        if !$prefix_include and FileTest.exists?(dir+"/R.h")
+            $prefix_include=dir
+        end
+    
+        if !$prefix_lib and FileTest.exists?(dir+"/lib/libR.so")
+            $prefix_lib=dir+"/lib"
+        end 
+    end
+    raise RuntimeError, "couldn't find R Home : R seems to be uninstalled!!" unless $prefix
+    raise RuntimeError, "couldn't find R.h!!" unless $prefix_include
+    raise RuntimeError, "couldn't find libR.so!!" unless $prefix_lib
+    #return multi
+  end  
+
+end
+
+
+def r4rb_makefile(inc,lib,version=nil) 
+    $CFLAGS = "-I"+inc+" -I."
+    $LDFLAGS = "-L"+lib if lib
+    $libs = "-lR"
+ 
+    header = nil
+
+    rb4r_name="R4rb"+((version and version!="orig") ? "."+version : "" )
+    $objs = [rb4r_name+".o"]
+
+    dir_config("R4rb")
+    create_makefile(rb4r_name)
+    File.rename("Makefile", "Makefile-#{version}")
+end
+
+## R is installed?
+find_installed_R
+
+$versions=["orig"] unless $versions
+$prefix,$prefix_include,$prefix_lib=[$prefix],[$prefix_include],[$prefix_lib] unless $prefix.is_a? Array
+
+modules = ""
+
+p $versions
+
+File.unlink("Makefile") if (FileTest.exist? "Makefile")
+$versions.each_with_index {|version,i| 
+    File.unlink("Makefile-#{version}") if (FileTest.exist? "Makefile-#{version}")
+    r4rb_makefile($prefix_include[i],$prefix_lib[i],version)
+    rb4r_name="R4rb"+((version and version!="orig") ? "."+version : "" )
+    modules += " #{rb4r_name}.#{CONFIG['DLEXT']}"
+    FileUtils.cp "R4rb.c", "#{rb4r_name}.c" if "R4rb.c" != "#{rb4r_name}.c"
+}
+
+open("Makefile", "w") {|f|
+    v = $nmake ? '{$(srcdir)}' : ''
+    f << "SHELL = /bin/sh" + "\n"
+    f << "srcdir = #{$srcdir}" + "\n"
+    f << "VPATH = $(srcdir)" + "\n"
+
+    f << "all: #{modules}" + "\n\n"
+
+    $versions.each do |version|
+        rb4r_name="R4rb"+((version and version!="orig") ? "."+version : "" )
+        f <<  "#{rb4r_name}.#{CONFIG['DLEXT']}: #{v}#{rb4r_name}.c" + "\n"
+        f << "\t@echo Now Making R4rb-#{version} extend module" + "\n"
+        f << "\t@$(MAKE) -f Makefile-#{version}" + "\n\n"
+    end
+
+    ["clean","distclean","install","site-install"].each do |task|
+        f << "#{task}:"
+        f << " "+modules if ["install","site-install"].include? task
+        f << "\n"
+        $versions.each do |version|
+            f << "\t@$(MAKE) -f Makefile-#{version} #{task}" + "\n"
+        end
+        f << "\n"
+    end
+   
+} 

data/lib/R2rb.rb

@@ -0,0 +1,5 @@
+require 'R4rb.so'
+require 'R4rb/R2rb_init'
+require 'R4rb/R2rb_eval'
+require 'R4rb/robj'
+require 'R4rb/converter'

data/lib/R4rb.rb

@@ -0,0 +1,59 @@
+# encoding: UTF-8
+Encoding.default_external = Encoding::UTF_8 unless RUBY_VERSION =~ /1\.8/
+# loading library: compatible for ruby-1.8.7, ruby-1.9.3, ruby-2.0.0
+if RUBY_PLATFORM=~/mingw32/ #because I did not manage to execute the same on mingw32
+  #   cmd=begin `Rscript`; rescue; "undefined";end
+  #   unless cmd=="undefined"
+  #   	cmd="Rscript.exe"
+  #   	version=`#{cmd} -e "cat(R.version$major,R.version$minor,sep='.')"`
+  #   else 
+  #   	if File.exists? (jsonfile=File.join(ENV["HOME"],"dyndoc","studio","win32","dyndoc.json"))
+		#    require 'json'
+		#    version=JSON.parse(File.read(jsonfile))["Rversion"]
+		# end
+  #   end
+  version=nil
+else
+	version=`Rscript -e 'cat(R.version$major,R.version$minor,sep=".")'`
+	version=version.split(".")[0...2].join(".")
+#puts version
+end
+
+found=nil
+[".bundle",".so"].each do |ext|
+	["","../ext/R4rb"].each do |path| #sometimes in lib sometimes in ext/R4rb/
+		lib=File.join(File.dirname(__FILE__),path,'R4rb'+(version ? '.'+version+ext : ext ) )
+		if File.exists? lib
+			puts "#{lib} found"
+			require lib
+			puts "#{lib} loaded"
+			found=true
+			break
+		end
+	end
+	break if found
+end
+
+# unless found #windows case
+# 	["i386","x64"].each do |version|
+# 		["","../ext/R4rb"].each do |path|
+# 			lib=File.join(File.dirname(__FILE__),path,'R4rb.'+version+'.so')
+# 			if File.exists? lib
+# 				puts "#{lib} found"
+# 				require lib
+# 				found=true
+# 				break
+# 			end
+# 		end
+# 	end
+# end
+
+require 'R4rb.so' unless found
+
+# loading ruby files
+require 'R4rb/R2rb_init'
+require 'R4rb/R2rb_eval'
+require 'R4rb/robj'
+require 'R4rb/Rserve'
+require 'R4rb/converter'
+require 'R4rb/R4rb'

data/lib/R4rb/R2rb_eval.rb

@@ -0,0 +1,116 @@
+# encoding: utf-8
+## Module R2rb
+
+module R2rb
+  def R2rb.eval(s,aff=nil)
+    s=["{\n"+s+"}\n"]
+    evalLines s,aff
+  end
+
+  def R2rb.parse(s,aff=nil)
+    s=["{\n"+s+"}\n"]
+    parseLines s,aff
+  end
+
+  def R2rb.try_eval(code)
+    try_code=".result_try_code<-try({\n"+code+"\n},silent=TRUE)\n.result_try_code"
+    R2rb << try_code
+    puts ".result_try_code".to_R if "inherits(.result_try_code,'try-error')".to_R
+  end
+
+
+  def R2rb.<<(s)
+    R2rb.eval(s)
+  end
+
+  class RVector
+
+    def <<(name)
+      if name.is_a? Symbol
+        @name=name.to_s
+        @type="var"
+      else
+        @name=name
+        @type="expr"
+      end
+      return self
+    end
+
+    def arg=(arg)
+      @arg=arg
+    end
+
+    #this method is the same as the previous one but return self! Let us notice that even by adding return self in the previous one
+    # I could not manage to execute (rvect.arg="[2]").value_with_arg but fortunately rvect.set_arg("[2]").value_with_arg is working!
+    def set_arg(arg)
+      @arg=arg
+      return self
+    end
+   
+    def >(arr)
+      res=self.get
+#puts "res";p @name;p res
+      if res
+#puts "arr.class:";p arr.class
+#puts "res.class";p res.class
+        res=[res] unless res.is_a? Array
+        arr.replace(res)
+      else
+        arr.clear
+      end
+      return self
+    end
+
+=begin #Done directly inside R4rb.c
+    def value_with_arg(arg)
+      old_name,old_type=@name.dup,@type.dup
+      @name,@type=@name+arg,"expr"
+      value
+      @name,@type=old_name,old_type
+    end
+=end
+
+  end
+
+  @@out=[]
+  ##@@out.rb2R=R2rb
+
+  def R2rb.<(rcode)
+    @@out.replace [] ##@@out=[] #important! it could otherwise remove
+    @@out.rb2R=self
+    @@out < rcode.to_s ##@@out.inR2rb rcode.to_s
+    return (@@out.length<=1 ? @@out[0] : @@out) 
+  end
+
+  class << self
+    alias output <
+  end
+
+  class Server
+    @@in,@@out=nil,[]
+
+    def Server.in
+      return @@in
+    end
+
+    def Server.in=(block)
+      @@in=block
+    end
+
+    def Server.<<(block)
+      @@in << block
+    end
+
+    def Server.out
+      return @@out.join("\n")
+    end
+    
+    def Server.echo(block=nil)
+      @@in=block if block
+      R2rb << ".output<<-capture.output({"+@@in+"})"
+      return (@@out < '.output').join("\n")
+    end
+  end
+
+end
+ 

data/lib/R4rb/R2rb_init.rb

@@ -0,0 +1,109 @@
+# encoding: utf-8
+
+##  Attention "...\n..." have to be replaced by "...\\n..."
+## example : 'cat("toto\n")' fails but not 'cat("toto\\n")'
+## more surprisingly, this fails even in comment '# cat("toto\n")'
+
+module R2rb
+
+  def R2rb.init(args=["--save","--slave","--quiet"])
+    @@initR=R2rb.initR(args) unless R2rb.alive?
+  end
+
+  def R2rb.alive?
+    defined? @@initR
+  end
+
+  class RBuffer
+    def initialize
+      @s=String.new
+    end
+    
+    def init
+      R2rb.init
+    end
+    
+    def clear
+      @s=""
+    end
+    
+    def +(s=nil)
+      if s
+      	s=s.to_s unless s.is_a? String
+      	@s += "\n"+s
+      else
+        clear
+      end
+      return self
+    end
+    
+    def exec(aff=nil)
+      R2rb.eval @s,aff
+    end
+  end
+
+ class RConsole
+   def initialize
+     require "readline"
+   end
+
+   def init args
+     R2rb.init args
+   end
+
+   def exec
+     #todo : continuation
+     toggle=true
+     fin=false
+     words=[]
+     rvect=R2rb::RVector.new("")
+     Readline.completion_proc=Proc.new {|e|
+       cpt=0
+       begin
+      	 begin
+      	   cpt += 1
+      	   toggle = !toggle
+      	   rvect << (toggle ? "apropos(" : "ls(pat=")+"'^"+e+"')" > words
+      	   res=words.map{|w| w[Regexp.new("^"+e+".*")]}-[nil]
+      	 end while res.empty? and cpt<3
+      	 res
+       rescue
+      	 warn("\r"+e+" not suitable for completion!!!")
+      	 []
+       end
+     }
+     Readline.completion_append_character=""
+     begin
+       line = Readline.readline("R> ", true)
+       if !(fin = line=="quit")
+      	 R2rb.eval line,true
+      	 toggle=true
+       end
+     end until fin
+   end
+ end
+end
+
+def find_installed_R
+
+  if RUBY_PLATFORM=~/mingw/ or RUBY_PLATFORM=~/msys/
+     ENV["R_HOME"]=`R RHOME`
+  elsif RUBY_PLATFORM=~/darwin/
+    ENV["R_HOME"]=`R RHOME`.strip
+  else
+    dirs=["/usr/lib/R","/usr/local/lib/R","/usr/lib64/R"]
+   
+    dirs.each do |dir|
+      if FileTest.exists?(dir)
+        return dir
+      end
+    end
+
+    raise RuntimeError, "couldn't find R Home : R seems to be uninstalled!!"
+  end
+
+end
+
+ENV["R_HOME"]=`R RHOME`.strip.split("\n").select{|l| l=~/^\//}[0] unless `R RHOME`.empty?
+
+ENV["R_HOME"]=find_installed_R unless ENV["R_HOME"]

data/lib/R4rb/R4rb.rb

@@ -0,0 +1,164 @@
+# encoding: utf-8
+class Object
+
+  def R4rb_is(mode)
+    unless [R2rb,Rserve,"R2rb","Rserve",:R2rb,:Rserve].include? mode
+      puts "Improper value for R4rb_is function!"
+      return 
+    end
+    unless mode.is_a? Module
+      mode=mode.to_s.to_sym
+      ##puts "R4rb_is: mode=#{mode}"
+      mode= case mode
+          when :R2rb
+            R2rb
+          when :Rserve
+            Rserve
+          end
+    end
+    if mode==Rserve and !Rserve.running?
+      puts "Rserve is not running and R4rb_is method cannot be set to :Rserve!"
+      mode=R2rb
+    end
+    ##p mode
+    ## trick to avoid warning when modifying constant!
+    con=Object #( self.is_a?(Module) ? self : self.class )
+    con.send(:remove_const, :R4rb) if con.const_defined?(:R4rb)
+    con.const_set(:R4rb, mode)
+  end
+
+  def R2rb_running?
+    Object.const_get(:R4rb)==R2rb
+  end
+
+  def Rserve_running?
+    Object.const_get(:R4rb)==Rserve
+  end
+
+  def R4rb_status?
+    puts "R is now in "+ ( R2rb_running? ? "local" : "server" )+" use!"
+  end
+
+end
+
+
+
+## first init
+unless Object.const_defined?(:R4rb)
+  ##puts "First, R4rb initialized to R2rb!"
+  R4rb_is R2rb 
+end
+
+=begin
+module R4rb
+
+  def R4rb.mode=(mode) #mode=:R4rb or :Rserve
+    return unless [:R2rb,:Rserve].include? mode
+    puts mode
+    puts Rserve
+    $R4rb=(mode==:R2rb ? R2rb : Rserve)
+    puts "R4rb mode changed: #{$R2rb.inspect}"
+  end
+
+  def R4rb.init(args=["--save","--slave","--quiet"])
+    R2rb.init(args)
+  end
+
+  def R4rb.<<(code)
+    $R4rb << code
+  end
+
+  def R4rb.<(code)
+    $R4rb < code
+  end
+
+  def R4rb.output(code)
+    $R4rb.output(code)
+  end
+
+
+  class << self
+    alias eval <<
+  end
+
+  RVector=$R4rb::RVector
+  
+end
+=end
+
+## reload 
+class String
+
+  def R2rb
+    R2rb < self
+  end
+
+  def Rserve(cli=nil)
+    Rserve < self
+  end
+
+  def R4rb
+    R4rb < self
+  end
+
+  alias to_R R4rb
+  alias evalR R4rb
+  alias Reval R4rb
+  alias R R4rb
+
+end
+
+class Array
+
+  def R2rb(var)
+    R2rb::RVector.assign(var.to_s,self)
+  end
+
+  def RServe(var,cli=nil)
+    Rserve::RVector.assign(var.to_s,self,cli)
+  end
+
+  def R4rb(var)
+    R4rb::RVector.assign(var.to_s,self)
+  end
+
+  alias to_R R4rb
+  alias evalR R4rb
+  alias Reval R4rb
+  alias R R4rb
+
+
+  #@@rb2R=nil
+
+  ## connect Array class to some RVector!!!
+  def Array.initR(init=true)
+    R2rb.init if init
+    #p @@rb2R
+  end
+
+  ## Here again to make this package self-content
+  def rb2R=(mode=nil)
+    ##puts "rb2R mode #{object_id}";p mode
+    mode=R4rb unless mode
+    return if @rb2R_mode and @rb2R_mode==mode
+    @rb2R_mode=mode unless @rb2R_mode
+    @rb2R=(@rb2R_mode==Rserve ? Rserve::RVector.new("") :  R2rb::RVector.new("") )
+    ##puts "rb2R=";p @rb2R
+  end
+
+  def >(outR) #outR represents here an R object
+    self.rb2R=nil unless @rb2R
+    @rb2R << outR
+    @rb2R < self
+    return self
+  end
+
+  def <(outR) #outR represents here an R expression to execute and put inside the Array
+    #p @rb2R
+    self.rb2R=nil unless @rb2R
+    @rb2R << outR
+    @rb2R > self
+    return self
+  end
+
+end